N-terminal Transmembrane-Helix Epitope Tag for X-ray Crystallography and Electron Microscopy of Small Membrane Proteins

McIlwain, Benjamin C.; Erwin, Amanda L.; Davis, Alexander R.; Ben Koff, B.; Chang, Louise; Bylund, Tatsiana; Chuang, Gwo-Yu; Kwong, Peter D.; Ohi, Melanie D.; Lai, Yen-Ting; Stockbridge, Randy B.

doi:10.1016/j.jmb.2021.166909

Title: N-terminal Transmembrane-Helix Epitope Tag for X-ray Crystallography and Electron Microscopy of Small Membrane Proteins

Journal Article · 31 July 2021 · Journal of Molecular Biology

DOI: https://doi.org/10.1016/j.jmb.2021.166909 · OSTI ID:1808603

McIlwain, Benjamin C.;

;

; Ben Koff, B.;

;

; Chuang, Gwo-Yu; Kwong, Peter D.;

; Lai, Yen-Ting;

Not Available

View Journal Article

Cite

Export

Save

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1808603

Journal Information:: Journal of Molecular Biology, Journal Name: Journal of Molecular Biology Journal Issue: 16 Vol. 433; ISSN 0022-2836

Publisher:: ElsevierCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (54)

Monobodies and other synthetic binding proteins for expanding protein science: Monobodies and Other Synthetic Binding Proteins Sha, Fern; Salzman, Gabriel; Gupta, Ankit Protein Science, Vol. 26, Issue 5 https://doi.org/10.1002/pro.3148	journal	March 2017
UCSF ChimeraX: Meeting modern challenges in visualization and analysis: UCSF ChimeraX Visualization System Goddard, Thomas D.; Huang, Conrad C.; Meng, Elaine C. Protein Science, Vol. 27, Issue 1 https://doi.org/10.1002/pro.3235	journal	September 2017
MolProbity: More and better reference data for improved all-atom structure validation: PROTEIN SCIENCE.ORG Williams, Christopher J.; Headd, Jeffrey J.; Moriarty, Nigel W. Protein Science, Vol. 27, Issue 1 https://doi.org/10.1002/pro.3330	journal	November 2017
Broadly Neutralizing Anti-HIV Antibody 4E10 Recognizes a Helical Conformation of a Highly Conserved Fusion-Associated Motif in gp41 Cardoso, Rosa M. F.; Zwick, Michael B.; Stanfield, Robyn L. Immunity, Vol. 22, Issue 2 https://doi.org/10.1016/j.immuni.2004.12.011	journal	February 2005
Crystallographic Identification of Lipid as an Integral Component of the Epitope of HIV Broadly Neutralizing Antibody 4E10 Irimia, Adriana; Sarkar, Anita; Stanfield, Robyn L. Immunity, Vol. 44, Issue 1 https://doi.org/10.1016/j.immuni.2015.12.001	journal	January 2016
Functional Contacts between MPER and the Anti-HIV-1 Broadly Neutralizing Antibody 4E10 Extend into the Core of the Membrane Rujas, Edurne; Insausti, Sara; García-Porras, Miguel Journal of Molecular Biology, Vol. 429, Issue 8 https://doi.org/10.1016/j.jmb.2017.03.008	journal	April 2017
Automated molecular microscopy: The new Leginon system Suloway, Christian; Pulokas, James; Fellmann, Denis Journal of Structural Biology, Vol. 151, Issue 1 https://doi.org/10.1016/j.jsb.2005.03.010	journal	July 2005
Automated electron microscope tomography using robust prediction of specimen movements Mastronarde, David N. Journal of Structural Biology, Vol. 152, Issue 1 https://doi.org/10.1016/j.jsb.2005.07.007	journal	October 2005
CTFFIND4: Fast and accurate defocus estimation from electron micrographs Rohou, Alexis; Grigorieff, Nikolaus Journal of Structural Biology, Vol. 192, Issue 2 https://doi.org/10.1016/j.jsb.2015.08.008	journal	November 2015
Gctf: Real-time CTF determination and correction Zhang, Kai Journal of Structural Biology, Vol. 193, Issue 1 https://doi.org/10.1016/j.jsb.2015.11.003	journal	January 2016
Development of imaging scaffolds for cryo-electron microscopy Yeates, Todd O.; Agdanowski, Matthew P.; Liu, Yuxi Current Opinion in Structural Biology, Vol. 60 https://doi.org/10.1016/j.sbi.2020.01.012	journal	February 2020
Cryo-electron microscopy analysis of small membrane proteins Nygaard, Rie; Kim, Jonathan; Mancia, Filippo Current Opinion in Structural Biology, Vol. 64 https://doi.org/10.1016/j.sbi.2020.05.009	journal	October 2020
Fabs Enable Single Particle cryoEM Studies of Small Proteins Wu, Shenping; Avila-Sakar, Agustin; Kim, JungMin Structure, Vol. 20, Issue 4 https://doi.org/10.1016/j.str.2012.02.017	journal	April 2012
Cork-in-Bottle Occlusion of Fluoride Ion Channels by Crystallization Chaperones McIlwain, Benjamin C.; Newstead, Simon; Stockbridge, Randy B. Structure, Vol. 26, Issue 4 https://doi.org/10.1016/j.str.2018.02.004	journal	April 2018
Structure of a prokaryotic virtual proton pump at 3.2 Å resolution Fang, Yiling; Jayaram, Hariharan; Shane, Tania Nature, Vol. 460, Issue 7258 https://doi.org/10.1038/nature08201	journal	July 2009
Broad and potent neutralization of HIV-1 by a gp41-specific human antibody Huang, Jinghe; Ofek, Gilad; Laub, Leo Nature, Vol. 491, Issue 7424 https://doi.org/10.1038/nature11544	journal	September 2012
Crystal structures of a double-barrelled fluoride ion channel Stockbridge, Randy B.; Kolmakova-Partensky, Ludmila; Shane, Tania Nature, Vol. 525, Issue 7570 https://doi.org/10.1038/nature14981	journal	September 2015
Cryo-EM structures of the TMEM16A calcium-activated chloride channel Dang, Shangyu; Feng, Shengjie; Tien, Jason Nature, Vol. 552, Issue 7685 https://doi.org/10.1038/nature25024	journal	December 2017
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination Punjani, Ali; Rubinstein, John L.; Fleet, David J. Nature Methods, Vol. 14, Issue 3 https://doi.org/10.1038/nmeth.4169	journal	February 2017
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy Zheng, Shawn Q.; Palovcak, Eugene; Armache, Jean-Paul Nature Methods, Vol. 14, Issue 4 https://doi.org/10.1038/nmeth.4193	journal	February 2017
Precise mapping of subunits in multiprotein complexes by a versatile electron microscopy label Flemming, Dirk; Thierbach, Karsten; Stelter, Philipp Nature Structural & Molecular Biology, Vol. 17, Issue 6 https://doi.org/10.1038/nsmb.1811	journal	May 2010
Crystal structure of a non-neutralizing antibody to the HIV-1 gp41 membrane-proximal external region Nicely, Nathan I.; Dennison, S. Moses; Spicer, Leonard Nature Structural & Molecular Biology, Vol. 17, Issue 12 https://doi.org/10.1038/nsmb.1944	journal	November 2010
High-resolution structure determination of sub-100 kDa complexes using conventional cryo-EM Herzik, Mark A.; Wu, Mengyu; Lander, Gabriel C. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-08991-8	journal	March 2019
An MPER antibody neutralizes HIV-1 using germline features shared among donors Zhang, Lei; Irimia, Adriana; He, Lingling Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12973-1	journal	November 2019
Synthetic antibodies against BRIL as universal fiducial marks for single−particle cryoEM structure determination of membrane proteins Mukherjee, Somnath; Erramilli, Satchal K.; Ammirati, Mark Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-15363-0	journal	March 2020
Antibody responses to viral infections: a structural perspective across three different enveloped viruses Murin, Charles D.; Wilson, Ian A.; Ward, Andrew B. Nature Microbiology, Vol. 4, Issue 5 https://doi.org/10.1038/s41564-019-0392-y	journal	March 2019
Cryo-EM structure of the insect olfactory receptor Orco Butterwick, Joel A.; del Mármol, Josefina; Kim, Kelly H. Nature, Vol. 560, Issue 7719 https://doi.org/10.1038/s41586-018-0420-8	journal	August 2018
Serotonin transporter–ibogaine complexes illuminate mechanisms of inhibition and transport Coleman, Jonathan A.; Yang, Dongxue; Zhao, Zhiyu Nature, Vol. 569, Issue 7754 https://doi.org/10.1038/s41586-019-1135-1	journal	April 2019
Structure and drug resistance of the Plasmodium falciparum transporter PfCRT Kim, Jonathan; Tan, Yong Zi; Wicht, Kathryn J. Nature, Vol. 576, Issue 7786 https://doi.org/10.1038/s41586-019-1795-x	journal	November 2019
Structure and mechanism of the ER-based glucosyltransferase ALG6 Bloch, Joël S.; Pesciullesi, Giorgio; Boilevin, Jérémy Nature, Vol. 579, Issue 7799 https://doi.org/10.1038/s41586-020-2044-z	journal	February 2020
Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM Uchański, Tomasz; Masiulis, Simonas; Fischer, Baptiste Nature Methods, Vol. 18, Issue 1 https://doi.org/10.1038/s41592-020-01001-6	journal	January 2021
Yeast surface display platform for rapid discovery of conformationally selective nanobodies McMahon, Conor; Baier, Alexander S.; Pascolutti, Roberta Nature Structural & Molecular Biology, Vol. 25, Issue 3 https://doi.org/10.1038/s41594-018-0028-6	journal	February 2018
SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM Wagner, Thorsten; Merino, Felipe; Stabrin, Markus Communications Biology, Vol. 2, Issue 1 https://doi.org/10.1038/s42003-019-0437-z	journal	June 2019
Human broadly neutralizing antibodies to the envelope glycoprotein complex of hepatitis C virus Giang, E.; Dorner, M.; Prentoe, J. C. Proceedings of the National Academy of Sciences, Vol. 109, Issue 16 https://doi.org/10.1073/pnas.1114927109	journal	April 2012
Structure of the Ebola virus envelope protein MPER/TM domain and its interaction with the fusion loop explains their fusion activity Lee, Jinwoo; Nyenhuis, David A.; Nelson, Elizabeth A. Proceedings of the National Academy of Sciences, Vol. 114, Issue 38 https://doi.org/10.1073/pnas.1708052114	journal	September 2017
Structure of the membrane proximal external region of HIV-1 envelope glycoprotein Fu, Qingshan; Shaik, Md Munan; Cai, Yongfei Proceedings of the National Academy of Sciences, Vol. 115, Issue 38 https://doi.org/10.1073/pnas.1807259115	journal	September 2018
Application of antihelix antibodies in protein structure determination Kim, Ji Won; Kim, Songwon; Lee, Haerim Proceedings of the National Academy of Sciences, Vol. 116, Issue 36 https://doi.org/10.1073/pnas.1910080116	journal	August 2019
Repurposing off-the-shelf antihelix antibodies for enabling structural biology Koide, Shohei Proceedings of the National Academy of Sciences, Vol. 116, Issue 36 https://doi.org/10.1073/pnas.1912643116	journal	August 2019
Single-particle cryo-electron microscopy of macromolecular complexes Skiniotis, Georgios; Southworth, Daniel R. Microscopy, Vol. 65, Issue 1 https://doi.org/10.1093/jmicro/dfv366	journal	November 2015
OPM database and PPM web server: resources for positioning of proteins in membranes Lomize, Mikhail A.; Pogozheva, Irina D.; Joo, Hyeon Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr703	journal	September 2011
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V. Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 5 https://doi.org/10.1107/S0907444908004319	journal	April 2008
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
REFMAC 5 for the refinement of macromolecular crystal structures Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911001314	journal	March 2011
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/S2059798319011471	journal	October 2019
Highly Conserved Protective Epitopes on Influenza B Viruses Dreyfus, C.; Laursen, N. S.; Kwaks, T. Science, Vol. 337, Issue 6100 https://doi.org/10.1126/science.1222908	journal	August 2012
Structure of a Glycerol-Conducting Channel and the Basis for Its Selectivity Fu, D. Science, Vol. 290, Issue 5491 https://doi.org/10.1126/science.290.5491.481	journal	October 2000
Potent and broad HIV-neutralizing antibodies in memory B cells and plasma Williams, LaTonya D.; Ofek, Gilad; Schätzle, Sebastian Science Immunology, Vol. 2, Issue 7 https://doi.org/10.1126/sciimmunol.aal2200	journal	January 2017
A Conformational Switch in Human Immunodeficiency Virus gp41 Revealed by the Structures of Overlapping Epitopes Recognized by Neutralizing Antibodies Pejchal, R.; Gach, J. S.; Brunel, F. M. Journal of Virology, Vol. 83, Issue 17 https://doi.org/10.1128/JVI.00685-09	journal	June 2009
Optimization of the Solubility of HIV-1-Neutralizing Antibody 10E8 through Somatic Variation and Structure-Based Design Kwon, Young D.; Georgiev, Ivelin S.; Ofek, Gilad Journal of Virology, Vol. 90, Issue 13 https://doi.org/10.1128/JVI.03246-15	journal	April 2016
Negative staining and image classification — powerful tools in modern electron microscopy Ohi, Melanie; Li, Ying; Cheng, Yifan Biological Procedures Online, Vol. 6, Issue 1 https://doi.org/10.1251/bpo70	journal	January 2004
Developmental Pathway of the MPER-Directed HIV-1-Neutralizing Antibody 10E8 Soto, Cinque; Ofek, Gilad; Joyce, M. Gordon PLOS ONE, Vol. 11, Issue 6 https://doi.org/10.1371/journal.pone.0157409	journal	June 2016
Lipid interactions and angle of approach to the HIV-1 viral membrane of broadly neutralizing antibody 10E8: Insights for vaccine and therapeutic design Irimia, Adriana; Serra, Andreia M.; Sarkar, Anita PLOS Pathogens, Vol. 13, Issue 2 https://doi.org/10.1371/journal.ppat.1006212	journal	February 2017
New tools for automated high-resolution cryo-EM structure determination in RELION-3 Zivanov, Jasenko; Nakane, Takanori; Forsberg, Björn O. eLife, Vol. 7 https://doi.org/10.7554/eLife.42166	journal	November 2018

Similar Records

N-terminal Transmembrane-Helix Epitope Tag for X-ray Crystallography and Electron Microscopy of Smal

Journal Article · 2021 · J. Mol. Biol. · OSTI ID:1814811

McIlwain, Benjamin C.; Erwin, Amanda L.; Davis, Alexander R.; +8 more

Epitope-dependent mechanisms of CD27 neutralization revealed by X-ray crystallography

Journal Article · 2017 · Molecular Immunology · OSTI ID:1413767

Obmolova, Galina; Teplyakov, Alexey; Malia, Thomas J.; +7 more

In meso in situ serial X-ray crystallography of soluble and membrane proteins

Journal Article · 2015 · Acta Crystallographica. Section D: Biological Crystallography · OSTI ID:22389068

Huang, Chia-Ying; Olieric, Vincent; Ma, Pikyee; +4 more

Title: N-terminal Transmembrane-Helix Epitope Tag for X-ray Crystallography and Electron Microscopy of Small Membrane Proteins

Citation Formats

References (54)

Similar Records

Related Subjects