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Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution

Journal Article · · Acta Crystallographica. Section D: Biological Crystallography
 [1];  [2];  [3];  [4];  [4];  [2];  [4];  [5];  [4];  [2];  [6];  [2];  [6];  [6];  [4];  [4];  [5];  [2]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering; DOE/OSTI
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Univ. of Cambridge (United Kingdom). Cambridge Inst. for Medical Research. Wellcome Trust. Dept. of Haematology
  4. Duke Univ., Durham, NC (United States). Medical Center. Dept. of Biochemistry
  5. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  6. Univ. of Cambridge (United Kingdom). Cambridge Inst. for Medical Research. Wellcome Trust. Dept. of Haematology
+ Show Author Affiliations

Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1625666
Journal Information:
Acta Crystallographica. Section D: Biological Crystallography, Journal Name: Acta Crystallographica. Section D: Biological Crystallography Journal Issue: 2 Vol. 66; ISSN 0907-4449
Publisher:
International Union of CrystallographyCopyright Statement
Country of Publication:
United States
Language:
English

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Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard journal December 2007
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Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation journal October 2019
Multiple conformations facilitate PilT function in the type IV pilus journal November 2019
Homologous bd oxidases share the same architecture but differ in mechanism journal November 2019
Assembly and substrate recognition of curli biogenesis system journal January 2020
Ultracompact 3D microfluidics for time-resolved structural biology journal January 2020
Structural insights into tetraspanin CD9 function journal March 2020
An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism journal June 2020
The biosynthetic origin of psychoactive kavalactones in kava journal July 2019
Protection of calves by a prefusion-stabilized bovine RSV F vaccine journal March 2017
A Pandas complex adapted for piRNA-guided transcriptional silencing and heterochromatin formation journal September 2019
Cryo-EM structure of the bacteria-killing type IV secretion system core complex from Xanthomonas citri journal October 2018
T3S injectisome needle complex structures in four distinct states reveal the basis of membrane coupling and assembly journal August 2019
Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates journal September 2019
Crystal structures of the gastric proton pump journal April 2018
Mechanism for remodelling of the cell cycle checkpoint protein MAD2 by the ATPase TRIP13 journal July 2018
Structures of the intermediates of Kok’s photosynthetic water oxidation clock journal November 2018
Structural basis of coreceptor recognition by HIV-1 envelope spike journal December 2018
Serotonin transporter–ibogaine complexes illuminate mechanisms of inhibition and transport journal April 2019
An ultra-stable gold-coordinated protein cage displaying reversible assembly journal May 2019
Structures of influenza A virus RNA polymerase offer insight into viral genome replication journal September 2019
Architecture of autoinhibited and active BRAF–MEK1–14-3-3 complexes journal October 2019
VISTA is an acidic pH-selective ligand for PSGL-1 journal October 2019
A mycobacterial ABC transporter mediates the uptake of hydrophilic compounds journal March 2020
A small-molecule inhibitor of C5 complement protein journal June 2019
Chain alignment of collagen I deciphered using computationally designed heterotrimers journal January 2020
Molecular basis for receptor tyrosine kinase A-loop tyrosine transphosphorylation journal January 2020
Structural basis for membrane anchoring and fusion regulation of the herpes simplex virus fusogen gB journal May 2018
Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation journal May 2018
Atg2 mediates direct lipid transfer between membranes for autophagosome formation journal March 2019
T cell receptor cross-reactivity between gliadin and bacterial peptides in celiac disease journal December 2019
MHz data collection of a microcrystalline mixture of different jack bean proteins journal April 2019
Conserved, unstructured regions in Pseudomonas aeruginosa PilO are important for type IVa pilus function journal February 2018
First insights of peptidoglycan amidation in Gram-positive bacteria - the high-resolution crystal structure of Staphylococcus aureus glutamine amidotransferase GatD journal March 2018
NADH/NADPH bi-cofactor-utilizing and thermoactive ketol-acid reductoisomerase from Sulfolobus acidocaldarius journal May 2018
Structural determinants of specificity and regulation of activity in the allosteric loop network of human KLK8/neuropsin journal July 2018
A fundamental catalytic difference between zinc and manganese dependent enzymes revealed in a bacterial isatin hydrolase journal August 2018
The first crystal structure of a DNA-free nuclear receptor DNA binding domain sheds light on DNA-driven allostery in the glucocorticoid receptor journal September 2018
Crystal structure of FlgL and its implications for flagellar assembly journal September 2018
Direct visualization of DNA baton pass between replication factors bound to PCNA journal November 2018
Search for efficient inhibitors of myotoxic activity induced by ophidian phospholipase A2-like proteins using functional, structural and bioinformatics approaches journal January 2019
Polyacrylamide injection matrix for serial femtosecond crystallography journal February 2019
Biochemical and structural characterization of tomato polyphenol oxidases provide novel insights into their substrate specificity journal March 2019
Structural bases of peptidoglycan recognition by lysostaphin SH3b domain journal April 2019
Structural and functional characterization of the PDZ domain of the human phosphatase PTPN3 and its interaction with the human papillomavirus E6 oncoprotein journal May 2019
Structural and biochemical characterization of Rv0187, an O-methyltransferase from Mycobacterium tuberculosis journal May 2019
X-ray Crystallographic Structure and Oligomerization of Gloeobacter Rhodopsin journal August 2019
Structure of Turnip mosaic virus and its viral-like particles journal October 2019
Structural understanding of the recycling of oxidized ascorbate by dehydroascorbate reductase (OsDHAR) from Oryza sativa L. japonica journal January 2016
Screening of saponins and sapogenins from Medicago species as potential PPARγ agonists and X-ray structure of the complex PPARγ/caulophyllogenin journal June 2016
Crystal structure of MytiLec, a galactose-binding lectin from the mussel Mytilus galloprovincialis with cytotoxicity against certain cancer cell types journal June 2016
Structural and functional characterization of the CAP domain of pathogen-related yeast 1 (Pry1) protein journal June 2016
Crystal structure of Sec10, a subunit of the exocyst complex journal January 2017
Mycofactocin-associated mycobacterial dehydrogenases with non-exchangeable NAD cofactors journal January 2017
Pyridylthiazole-based ureas as inhibitors of Rho associated protein kinases (ROCK1 and 2) journal January 2012
Predicting protein–ligand binding affinity and correcting crystal structures with quantum mechanical calculations: lactate dehydrogenase A journal January 2019
Structural and functional studies on the extracellular domain of BST2/tetherin in reduced and oxidized conformations journal September 2010
Ligand-gated diffusion across the bacterial outer membrane journal May 2011
Crystal structure of lactose permease in complex with an affinity inactivator yields unique insight into sugar recognition journal May 2011
Structure and function of multiple Ca2+-binding sites in a K+ channel regulator of K+ conductance (RCK) domain journal October 2011
Crystal structure of the hybrid state of ribosome in complex with the guanosine triphosphatase release factor 3 journal September 2011
Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis journal October 2011
Structure of the VirB4 ATPase, alone and bound to the core complex of a type IV secretion system journal June 2012
Molecular basis for the action of the collagen-specific chaperone Hsp47/SERPINH1 and its structure-specific client recognition journal July 2012
T box RNA decodes both the information content and geometry of tRNA to affect gene expression journal April 2013
Structure of the C-terminal region of an ERG channel and functional implications journal June 2013
Structure and assembly of an inner membrane platform for initiation of type IV pilus biogenesis journal November 2013
PILR  and PILR  have a siglec fold and provide the basis of binding to sialic acid journal May 2014
Molecular basis for AUXIN RESPONSE FACTOR protein interaction and the control of auxin response repression journal March 2014
Formation and structures of GroEL:GroES2 chaperonin footballs, the protein-folding functional form journal August 2014
An intramolecular lock facilitates folding and stabilizes the tertiary structure of Streptococcus mutans adhesin P1 journal October 2014
Structural basis for inhibition of TLR2 by staphylococcal superantigen-like protein 3 (SSL3) journal August 2015
Cryo-EM structures elucidate neutralizing mechanisms of anti-chikungunya human monoclonal antibodies with therapeutic activity journal October 2015
Inhibition of SCF ubiquitin ligases by engineered ubiquitin variants that target the Cul1 binding site on the Skp1–F-box interface journal March 2016
Aurone synthase is a catechol oxidase with hydroxylase activity and provides insights into the mechanism of plant polyphenol oxidases journal March 2016
Role of bacteriophage T4 baseplate in regulating assembly and infection journal February 2016
Structures of the nucleoid occlusion protein SlmA bound to DNA and the C-terminal domain of the cytoskeletal protein FtsZ journal April 2016
Asymmetric cryo-EM structure of the canonical Allolevivirus Qβ reveals a single maturation protein and the genomic ssRNA in situ journal September 2016
Clues to the mechanism of cholesterol transfer from the structure of NPC1 middle lumenal domain bound to NPC2 journal August 2016
IP 3 -mediated gating mechanism of the IP 3 receptor revealed by mutagenesis and X-ray crystallography journal April 2017
Covalent inhibitors for eradication of drug-resistant HIV-1 reverse transcriptase: From design to protein crystallography journal August 2017
Targeting cancer addiction for SALL4 by shifting its transcriptome with a pharmacologic peptide journal July 2018
Structural basis for activation of voltage sensor domains in an ion channel TPC1 journal September 2018
Molecular mechanism of activation of the immunoregulatory amidase NAAA journal October 2018
Structural, functional, and behavioral insights of dopamine dysfunction revealed by a deletion in SLC6A3 journal February 2019
Structures of ligand-occupied β-Klotho complexes reveal a molecular mechanism underlying endocrine FGF specificity and activity journal April 2019
Structural basis for adenylation and thioester bond formation in the ubiquitin E1 journal June 2019
In situ structures of RNA-dependent RNA polymerase inside bluetongue virus before and after uncoating journal July 2019
Structural Determination of Functional Domains in Early B-cell Factor (EBF) Family of Transcription Factors Reveals Similarities to Rel DNA-binding Proteins and a Novel Dimerization Motif* journal August 2010
Structure-guided Mutation of the Conserved G3-box Glycine in Rheb Generates a Constitutively Activated Regulator of Mammalian Target of Rapamycin (mTOR) journal May 2014
Crystal Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1) Zinc Fingers Bound to DNA: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO DNA-DEPENDENT PARP-1 ACTIVITY journal January 2011
Crystal Structures of Bacterial Peptidoglycan Amidase AmpD and an Unprecedented Activation Mechanism* journal September 2011
Structure of a Ternary Naa50p (NAT5/SAN) N-terminal Acetyltransferase Complex Reveals the Molecular Basis for Substrate-specific Acetylation journal September 2011
The Crystal Structure of the Protein-Disulfide Isomerase Family Member ERp27 Provides Insights into Its Substrate Binding Capabilities journal January 2013
Histone Deacetylase (HDAC) Inhibitor Kinetic Rate Constants Correlate with Cellular Histone Acetylation but Not Transcription and Cell Viability journal July 2013
Rational Design of Broad Spectrum Antibacterial Activity Based on a Clinically Relevant Enoyl-Acyl Carrier Protein (ACP) Reductase Inhibitor journal June 2014
Cocrystal Structures of Glycyl-tRNA Synthetase in Complex with tRNA Suggest Multiple Conformational States in Glycylation journal June 2014
SbnG, a Citrate Synthase in Staphylococcus aureus : A NEW FOLD ON AN OLD ENZYME journal October 2014
Structural Basis for the Disruption of the Cerebral Cavernous Malformations 2 (CCM2) Interaction with Krev Interaction Trapped 1 (KRIT1) by Disease-associated Mutations journal January 2015
Structural Characterization of Bardet-Biedl Syndrome 9 Protein (BBS9) journal August 2015
Ligand-induced Dimerization of Middle East Respiratory Syndrome (MERS) Coronavirus nsp5 Protease (3CLpro) journal August 2015
Structural Hot Spots Determine Functional Diversity of the Candida glabrata Epithelial Adhesin Family journal August 2015
Structural Insights into the Carbohydrate Binding Ability of an α-(1→2) Branching Sucrase from Glycoside Hydrolase Family 70 journal April 2016
PilN Binding Modulates the Structure and Binding Partners of the Pseudomonas aeruginosa Type IVa Pilus Protein PilM journal May 2016
i-bodies, Human Single Domain Antibodies That Antagonize Chemokine Receptor CXCR4 journal April 2016
Structural Basis of Host Autophagy-related Protein 8 (ATG8) Binding by the Irish Potato Famine Pathogen Effector Protein PexRD54 journal September 2016
Distinct Features of Cyanophage-encoded T-type Phycobiliprotein Lyase ΦCpeT: THE ROLE OF AUXILIARY METABOLIC GENES journal February 2017
Live-cell visualization of gasdermin D-driven pyroptotic cell death journal September 2017
Dual functionality of β-tryptase protomers as both proteases and cofactors in the active tetramer journal June 2018
The partial dissociation of MHC class I–bound peptides exposes their N terminus to trimming by endoplasmic reticulum aminopeptidase 1 journal March 2018
Mycolyltransferase from Mycobacterium tuberculosis in covalent complex with tetrahydrolipstatin provides insights into antigen 85 catalysis journal January 2018
Distinctive phosphoinositide- and Ca2+-binding properties of normal and cognitive performance–linked variant forms of KIBRA C2 domain journal June 2018
Minimalism and functionality: Structural lessons from the heterodimeric N4 bacteriophage RNA polymerase II journal August 2018
Structures of human cytochrome P450 1A1 with bergamottin and erlotinib reveal active-site modifications for binding of diverse ligands journal September 2018
Cryo-EM structure of the NLRC4CARD filament provides insights into how symmetric and asymmetric supramolecular structures drive inflammasome assembly journal December 2018
Crystal structure of the complex between venom toxin and serum inhibitor from Viperidae snake journal January 2019
Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates journal February 2019
Crystal structure of a Y-box binding protein 1 (YB-1)–RNA complex reveals key features and residues interacting with RNA journal July 2019
The 1.9 Å crystal structure of the extracellular matrix protein Bap1 from Vibrio cholerae provides insights into bacterial biofilm adhesion journal October 2019
A molecular model for self-assembly of the synaptonemal complex protein SYCE3 journal June 2019
Productive reorientation of a bound oxime reactivator revealed in room temperature X-ray structures of native and VX-inhibited human acetylcholinesterase journal May 2019
Structural insights into the mechanism of c-di-GMP–bound YcgR regulating flagellar motility in Escherichia coli journal December 2019
Interaction of the tetratricopeptide repeat domain of aryl hydrocarbon receptor–interacting protein–like 1 with the regulatory Pγ subunit of phosphodiesterase 6 journal October 2019
Structural basis for the specific cleavage of core-fucosylated N -glycans by endo-β- N -acetylglucosaminidase from the fungus Cordyceps militaris journal September 2019
The structure of the bacterial iron–catecholate transporter Fiu suggests that it imports substrates via a two-step mechanism journal December 2019
Molecular interactions between sex hormone–binding globulin and nonsteroidal ligands that enhance androgen activity journal December 2019
Structural mechanism of the phosphorylation-dependent dimerization of the MDC1 forkhead-associated domain journal January 2012
Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract journal September 2012
On the structural basis and design guidelines for type II topoisomerase-targeting anticancer drugs journal September 2013
The structure of Rpf2–Rrs1 explains its role in ribosome biogenesis journal June 2015
Nop9 binds the central pseudoknot region of 18S rRNA journal January 2017
NS3 helicase from dengue virus specifically recognizes viral RNA sequence to ensure optimal replication journal November 2017
Tethering not required: the glucocorticoid receptor binds directly to activator protein-1 recognition motifs to repress inflammatory genes journal June 2017
Crystallographic analyses illustrate significant plasticity and efficient recoding of meganuclease target specificity journal June 2017
Human Argonaute3 has slicer activity journal October 2017
Structural analysis of fungal CENP-H/I/K homologs reveals a conserved assembly mechanism underlying proper chromosome alignment journal November 2018
Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site journal December 2018
Expanding RNA binding specificity and affinity of engineered PUF domains journal February 2018
A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance journal March 2018
Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction journal May 2018
TraN: A novel repressor of an Enterococcus conjugative type IV secretion system journal July 2018
A unique intra-molecular fidelity-modulating mechanism identified in a viral RNA-dependent RNA polymerase journal September 2018
Double autoinhibition mechanism of signal transduction ATPases with numerous domains (STAND) with a tetratricopeptide repeat sensor journal February 2019
Toxin–antitoxin operon kacAT of Klebsiella pneumoniae is regulated by conditional cooperativity via a W-shaped KacA–KacT complex journal July 2019
Structural and functional insight into the Mycobacterium tuberculosis protein PrpR reveals a novel type of transcription factor journal August 2019
A polar filter in DNA polymerases prevents ribonucleotide incorporation journal September 2019
Crystal structure of an assembly intermediate of respiratory Complex II journal April 2018
Structural Basis For Antigenic Peptide Precursor Processing by the Endoplasmic Reticulum Aminopeptidase ERAP1 journal April 2011
Dynein light chain 8a of Toxoplasma gondii , a unique conoid‐localized β‐strand‐swapped homodimer, is required for an efficient parasite growth journal December 2012
Asymmetric functions of a binuclear metal center within the transport pathway of a human zinc transporter ZIP4 journal November 2019
Symmetry broken and rebroken during the ATP hydrolysis cycle of the mitochondrial Hsp90 TRAP1 posted_content February 2017
Overcoming insecticide resistance through computational inhibitor design posted_content January 2019
The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand journal April 2018
Structural and functional studies of the RBPJ-SHARP complex reveal conserved corepressor binding site posted_content May 2018
Crystal structure of arginine-bound lysosomal transporter SLC38A9 in the cytosol-open state posted_content March 2018
Discovery of a novel stereospecific β-hydroxyacyl-CoA lyase/thioesterase shared by three metabolic pathways in Mycobacterium tuberculosis posted_content January 2018
Eradication of ENO1 -deleted Glioblastoma through Collateral Lethality posted_content January 2018
Structures in multiple conformations reveal distinct transition metal and proton pathways in an Nramp transporter posted_content January 2018
Karyopherin Kap114p regulates TATA-binding protein-mediated transcription posted_content September 2018
The Structure of Oxalate Decarboxylase at its Active pH posted_content September 2018
Structural basis for prodrug recognition by the SLC15 family of proton coupled peptide transporters posted_content January 2018
Structure of a bacterial ATP synthase posted_content November 2018
Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase posted_content January 2019
KLK4 inhibition by cyclic and acyclic peptides: structural and dynamical insights into standard-mechanism protease inhibitors posted_content January 2019
Structure-guided enhancement of selectivity of chemical probe inhibitors targeting bacterial seryl-tRNA synthetase posted_content January 2019
Role of coiled-coil registry shifts in activation of human Bicaudal D2 for dynein recruitment upon cargo-binding posted_content January 2019
Structural and functional characterisation of SiiA, an auxiliary protein from the SPI4-encoded type 1 secretion system from Salmonella enterica posted_content January 2019
Chemogenetic Control of Nanobodies journal January 2019
Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms posted_content August 2019
Thrombospondin module 1 domain (TSP1) of the matricellular protein CCN3 shows an atypical disulfide pattern and incomplete CWR layers posted_content January 2019
Ensemble cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation posted_content October 2019
A stable leading strand polymerase/clamp loader complex is required for normal and perturbed eukaryotic DNA replication posted_content January 2019
Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation posted_content January 2019
A cooperative network of molecular “hot spots” highlights the complexity of LH3 collagen glycosyltransferase activities posted_content April 2020
Wnt5a promotes Frizzled-4 signalosome assembly by stabilizing cysteine-rich domain dimerization journal May 2017
Structural and functional analysis of Rv0554 from Mycobacterium tuberculosis : testing a putative role in menaquinone biosynthesis journal July 2010
Perdeuteration: improved visualization of solvent structure in neutron macromolecular crystallography journal November 2014
The high-resolution crystal structure of phosphatidylinositol 4-kinase IIβ and the crystal structure of phosphatidylinositol 4-kinase IIα containing a nucleoside analogue provide a structural basis for isoform-specific inhibitor design journal June 2015
A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions journal September 2015
Stable sample delivery in viscous media via a capillary for serial crystallography journal February 2020
IPCAS : a direct-method-based pipeline from phasing to model building and refinement for macromolecular structure determination journal February 2020
Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both journal June 2019
A multicrystal diffraction data-collection approach for studying structural dynamics with millisecond temporal resolution journal October 2016
Fixed-target serial oscillation crystallography at room temperature text January 2019
High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source journal April 2019
A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography journal April 2019
Structure of the catalytic domain of Mre11 from Chaetomium thermophilum journal May 2015
Crystal structure of d(CCGGGGTACCCCGG) 2 at 1.4 Å resolution journal April 2017
Structure of an Influenza A virus N9 neuraminidase with a tetrabrachion-domain stalk journal January 2019
Crystal structure of the inhibitor-free form of the serine protease kallikrein-4 journal July 2019
Structure of an RNA helix with pyrimidine mismatches and cross-strand stacking journal September 2019
In-vacuum long-wavelength macromolecular crystallography journal March 2016
The 1.1 Å resolution structure of a periplasmic phosphate-binding protein from Stenotrophomonas maltophilia : a crystallization contaminant identified by molecular replacement using the entire Protein Data Bank journal July 2016
Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5′ mismatches journal July 2018
Introducing SEC–SANS for studies of complex self-organized biological systems journal November 2018
Resolving indexing ambiguities in X-ray free-electron laser diffraction patterns journal February 2019
Conformational changes in the third PDZ domain of the neuronal postsynaptic density protein 95 journal March 2019
Rare earth metals are essential for methanotrophic life in volcanic mudpots: Rare earth metals essential for methanotrophic life journal September 2013
Crystal structures of VIM‐1 complexes explain active site heterogeneity in VIM‐class metallo‐β‐lactamases journal November 2018
Structural basis for protein phosphatase 1 recruitment by glycogen‐targeting subunits journal November 2018
Crystal structure and activation mechanism of DR3 death domain journal April 2019
Structural basis for the recognition of MucA by MucB and AlgU in Pseudomonas aeruginosa journal July 2019
Structural insights into polysaccharide recognition by Flavobacterium johnsoniae dextranase, a member of glycoside hydrolase family 31 journal October 2019
Structural and biochemical characterization of a family 7 highly thermostable endoglucanase from the fungus Rasamsonia emersonii journal December 2019
Crystal structures and calorimetry reveal catalytically relevant binding mode of coproporphyrin and coproheme in coproporphyrin ferrochelatase journal December 2019
Energy landscape of domain motion in glutamate dehydrogenase deduced from cryo‐electron microscopy journal February 2020
Structural analysis, enzymatic characterization, and catalytic mechanisms of β-galactosidase from Bacillus circulans sp. alkalophilus: β-galactosidase from Bacillus circulans sp. alkalophilus journal March 2012
The 3.2 Å structure of a bioengineered variant of blood coagulation factor VIII indicates two conformations of the C2 domain journal September 2019
Structural and biochemical characterization of EDTA monooxygenase and its physical interaction with a partner flavin reductase: Characterization of EmoA from Chelativorans sp. BNC1 journal April 2016
Novel molecular insights into the anti‐oxidative stress response and structure–function of a salt‐inducible cyanobacterial Mn‐catalase journal June 2019
Structural insights into the lipid transfer mechanism of a non‐specific lipid transfer protein journal January 2020
Using Cryo-EM to Map Small Ligands on Dynamic Metabolic Enzymes: Studies with Glutamate Dehydrogenase journal April 2016
First High-Resolution Crystal Structures of the Glucocorticoid Receptor Ligand-Binding Domain–Peroxisome Proliferator-Activated γ Coactivator 1- α Complex with Endogenous and Synthetic Glucocorticoids journal August 2019
Structure and mechanism of human PrimPol, a DNA polymerase with primase activity journal October 2016
Cryo-EM structure of phosphodiesterase 6 reveals insights into the allosteric regulation of type I phosphodiesterases journal February 2019
pH-dependent gating mechanism of the Helicobacter pylori urea channel revealed by cryo-EM journal March 2019
Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors journal September 2019
Structure and genome ejection mechanism of Staphylococcus aureus phage P68 journal October 2019
Evolutionary adaptation in fucosyllactose uptake systems supports bifidobacteria-infant symbiosis journal August 2019
Blocking FcRn in humans reduces circulating IgG levels and inhibits IgG immune complex–mediated immune responses journal December 2019
The structure of Photosystem I acclimated to far-red light illuminates an ecologically important acclimation process in photosynthesis journal February 2020
Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding journal July 2011
Structural Insight into the Ion-Exchange Mechanism of the Sodium/Calcium Exchanger journal February 2012
The Crystal Structure of Human Argonaute2 journal April 2012
Control of Ribosomal Subunit Rotation by Elongation Factor G journal June 2013
Structures and Receptor Binding of Hemagglutinins from Human-Infecting H7N9 Influenza Viruses journal September 2013
Genetic and Molecular Basis of Drug Resistance and Species-Specific Drug Action in Schistosome Parasites journal November 2013
Structure-Based Design of a Fusion Glycoprotein Vaccine for Respiratory Syncytial Virus journal October 2013
Hepatitis C Virus E2 Envelope Glycoprotein Core Structure journal November 2013
Serial Femtosecond Crystallography of G Protein-Coupled Receptors journal December 2013
Structures of netrin-1 bound to two receptors provide insight into its axon guidance mechanism journal May 2014
Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine journal January 2015
Structural basis for histone H2B deubiquitination by the SAGA DUB module journal February 2016
Structure of the voltage-gated K+ channel Eag1 reveals an alternative voltage sensing mechanism journal August 2016
Structural basis for the gating mechanism of the type 2 ryanodine receptor RyR2 journal September 2016
DNA-PKcs structure suggests an allosteric mechanism modulating DNA double-strand break repair journal February 2017
Structure of a symmetric photosynthetic reaction center–photosystem journal July 2017
Structure of the complete elongation complex of RNA polymerase II with basal factors journal September 2017
Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis journal March 2018
De novo design of self-assembling helical protein filaments journal November 2018
Structural basis for blue-green light harvesting and energy dissipation in diatoms journal February 2019
eIF2B-catalyzed nucleotide exchange and phosphoregulation by the integrated stress response journal May 2019
A human postcatalytic spliceosome structure reveals essential roles of metazoan factors for exon ligation journal January 2019
Structural insights into TRPM8 inhibition and desensitization journal September 2019
Preferential induction of cross-group influenza A hemagglutinin stem–specific memory B cells after H7N9 immunization in humans journal July 2017
Structural Basis of Metallo-β-Lactamase Inhibition by Captopril Stereoisomers journal October 2015
Structural and Functional Characterization of an Electron Transfer Flavoprotein Involved in Toluene Degradation in Strictly Anaerobic Bacteria journal August 2019
Biochemical and Structural Studies of the Mycobacterium tuberculosis O6-Methylguanine Methyltransferase and Mutated Variants journal April 2013
Structure of Severe Fever with Thrombocytopenia Syndrome Virus Nucleocapsid Protein in Complex with Suramin Reveals Therapeutic Potential journal April 2013
Structural Basis of Nanobodies Targeting the Prototype Norovirus journal March 2019
Human Norovirus Neutralized by a Monoclonal Antibody Targeting the Histo-Blood Group Antigen Pocket journal December 2018
Structural Analysis of a Viral Ovarian Tumor Domain Protease from the Crimean-Congo Hemorrhagic Fever Virus in Complex with Covalently Bonded Ubiquitin journal January 2011
Structure of a Classical Broadly Neutralizing Stem Antibody in Complex with a Pandemic H2 Influenza Virus Hemagglutinin journal April 2013
Structural Basis for Linezolid Binding Site Rearrangement in the Staphylococcus aureus Ribosome journal May 2017
Structural Basis for the Differential Regulatory Roles of the PDZ Domain in C-Terminal Processing Proteases journal August 2019
Interaction of the Ankyrin H Core Effector of Legionella with the Host LARP7 Component of the 7SK snRNP Complex journal August 2019
Targeting Mannitol Metabolism as an Alternative Antimicrobial Strategy Based on the Structure-Function Study of Mannitol-1-Phosphate Dehydrogenase in Staphylococcus aureus journal August 2019
Probing Dominant Negative Behavior of Glucocorticoid Receptor β through a Hybrid Structural and Biochemical Approach journal April 2018
Structural and Functional Analysis of Pyrimidine Nucleoside Phosphorylases of the NP-I and NP-II Families in Complexes with 6-Methyluracil journal May 2018
Human VP8* mAbs neutralize rotavirus selectively in human intestinal epithelial cells journal August 2019
Crystal structure and DNA binding activity of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291 journal October 2016
Crystal structure of human S100A8 in complex with zinc and calcium journal June 2016
Crystal structure of carbonic anhydrase CaNce103p from the pathogenic yeast Candida albicans journal October 2018
Crystal structure of diamondback moth ryanodine receptor Repeat34 domain reveals insect-specific phosphorylation sites journal October 2019
Structural analysis and insertion study reveal the ideal sites for surface displaying foreign peptides on a betanodavirus-like particle journal January 2016
Structural insights into the substrate specificity of two esterases from the thermophilic Rhizomucor miehei journal June 2015
Crystal structures of a llama VHH antibody BCD090-M2 targeting human ErbB3 receptor journal January 2018
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community) journal January 2020
Structural and Mechanistic Basis of Zinc Regulation Across the E. coli Zur Regulon journal November 2014
Spliceosomal Prp8 intein at the crossroads of protein and RNA splicing journal October 2019
Chromatin Insulator Factors Involved in Long-Range DNA Interactions and Their Role in the Folding of the Drosophila Genome journal August 2014
Structural Studies of the Tandem Tudor Domains of Fragile X Mental Retardation Related Proteins FXR1 and FXR2 journal November 2010
Structure and function of a CE4 deacetylase isolated from a marine environment journal November 2017
Structural and functional analysis of Utp24, an endonuclease for processing 18S ribosomal RNA journal April 2018
Structural study reveals the temperature-dependent conformational flexibility of Tk-PTP, a protein tyrosine phosphatase from Thermococcus kodakaraensis KOD1 journal May 2018
Divalent cation and chloride ion sites of chicken acid sensing ion channel 1a elucidated by x-ray crystallography journal August 2018
Crystal structure of the major quadruplex formed in the promoter region of the human c-MYC oncogene journal October 2018
Crystal structure and functional characterization of a cold-active acetyl xylan esterase (PbAcE) from psychrophilic soil microbe Paenibacillus sp. journal October 2018
Structures of TOG1 and TOG2 from the human microtubule dynamics regulator CLASP1 journal July 2019
Crystal structure of L-aspartate aminotransferase from Schizosaccharomyces pombe journal August 2019
Structural Basis for the Inhibition of Histone Deacetylase 8 (HDAC8), a Key Epigenetic Player in the Blood Fluke Schistosoma mansoni journal September 2013
New World Bats Harbor Diverse Influenza A Viruses journal October 2013
Structural Insights into SraP-Mediated Staphylococcus aureus Adhesion to Host Cells journal June 2014
P. aeruginosa SGNH Hydrolase-Like Proteins AlgJ and AlgX Have Similar Topology but Separate and Distinct Roles in Alginate Acetylation journal August 2014
Structural and Functional Analysis of Murine Polyomavirus Capsid Proteins Establish the Determinants of Ligand Recognition and Pathogenicity journal October 2015
Three mutations switch H7N9 influenza to human-type receptor specificity journal June 2017
Structure of the Cladosporium fulvum Avr4 effector in complex with (GlcNAc)6 reveals the ligand-binding mechanism and uncouples its intrinsic function from recognition by the Cf-4 resistance protein journal August 2018
Structure-guided disruption of the pseudopilus tip complex inhibits the Type II secretion in Pseudomonas aeruginosa journal October 2018
Structure and mechanism of TagA, a novel membrane-associated glycosyltransferase that produces wall teichoic acids in pathogenic bacteria journal April 2019
Dynamic rotation of the protruding domain enhances the infectivity of norovirus journal July 2020
CENP ‐C unwraps the human CENP ‐A nucleosome through the H2A C‐terminal tail journal September 2019
Serial protein crystallography in an electron microscope text January 2020
The N-terminal domains of FLASH and Lsm11 form a 2:1 heterotrimer for histone pre-mRNA 3’-end processing text January 2017
Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF. text January 2016
Structure-based mechanism of cysteinyl leukotriene receptor inhibition by antiasthmatic drugs text January 2019
Design and synthesis of imidazole and triazole pyrazoles as Mycobacterium tuberculosis CYP121A1 inhibitors. text January 2020
Structural insights into the assembly and regulation of distinct viral capsid complexes text January 2020
Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5 journal March 2019
The Redox State Regulates the Conformation of Rv2466c to Activate the Antitubercular Prodrug TP053 text January 2015
Myelin 2′,3′-Cyclic Nucleotide 3′-Phosphodiesterase: Active-Site Ligand Binding and Molecular Conformation text January 2012
CH‐π Interactions Promote the Conversion of Hydroxypyruvate in a Class II Pyruvate Aldolase text January 2019
The Role of a Key Amino Acid Position in Species-Specific Proteinaceous dUTPase Inhibition journal June 2019
Architecture of the Bacterial Flagellar Distal Rod and Hook of Salmonella journal July 2019
High-Resolution Crystal Structure of RpoS Fragment including a Partial Region 1.2 and Region 2 from the Intracellular Pathogen Legionella pneumophila journal January 2018
Crystal Growth in Gels from the Mechanisms of Crystal Growth to Control of Polymorphism: New Trends on Theoretical and Experimental Aspects journal August 2019
Polysaccharide-Based Injection Matrix for Serial Crystallography journal May 2020
Crystal Structure of Human EOLA1 Implies Its Possibility of RNA Binding journal September 2019
Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon text January 2016
Structural basis of inhibition of lipid-linked oligosaccharide flippase PglK by a conformational nanobody text January 2017
Structural insight into substrate and inhibitor discrimination by human P-glycoprotein text January 2019
A Common Single Nucleotide Polymorphism in Endoplasmic Reticulum Aminopeptidase 2 Induces a Specificity Switch That Leads to Altered Antigen Processing journal July 2012
Crystal Structure of the Labile Complex of IL-24 with the Extracellular Domains of IL-22R1 and IL-20R2 journal August 2018
Structural and Functional Basis for LILRB Immune Checkpoint Receptor Recognition of HLA-G Isoforms journal November 2019
Directed evolution of artificial metalloenzymes for in vivo metathesis text January 2016
Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography text January 2017
Scaffold nucleoporins Nup188 and Nup192 share structural and functional properties with nuclear transport receptors journal June 2013
A new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5 Å resolution journal December 2013
Three-dimensional electron crystallography of protein microcrystals journal November 2013
GE23077 binds to the RNA polymerase ‘i’ and ‘i+1’ sites and prevents the binding of initiating nucleotides journal April 2014
Structural evidence for Scc4-dependent localization of cohesin loading journal June 2015
The structure of plant photosystem I super-complex at 2.8 Å resolution journal June 2015
Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments journal December 2015
Architecture and RNA binding of the human negative elongation factor journal June 2016
Patient-specific mutations impair BESTROPHIN1’s essential role in mediating Ca2+-dependent Cl- currents in human RPE journal October 2017
Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme journal March 2018
TMEM266 is a functional voltage sensor regulated by extracellular Zn2+ journal February 2019
tRNA ligase structure reveals kinetic competition between non-conventional mRNA splicing and mRNA decay journal June 2019
Ctf4 organizes sister replisomes and Pol α into a replication factory journal October 2019
De novo design of a homo-trimeric amantadine-binding protein journal December 2019
Ternary structure of the outer membrane transporter FoxA with resolved signalling domain provides insights into TonB-mediated siderophore uptake journal August 2019
Structure of the human BBSome core complex journal January 2020

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59 BASIC BIOLOGICAL SCIENCES
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Macromolecular Crystallography
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