Structural basis of CD4 downregulation by HIV-1 Nef

Kwon, Yonghwa; Kaake, Robyn M.; Echeverria, Ignacia; Suarez, Marissa; Shamsabadi , Mohammad Karimian; Stoneham, Charlotte; Ramirez, Peter W.; Kress, Jacob; Singh, Rajendra; Sali, Andrej; Krogan , Nevan; Guatelli, John; Jia , Xiaofei

doi:10.1038/s41594-020-0463-z

Structural basis of CD4 downregulation by HIV-1 Nef

Journal Article · 01 September 2020 · Nat. Struct. Mol. Biol.

DOI:https://doi.org/10.1038/s41594-020-0463-z· OSTI ID:1836770

Kwon, Yonghwa; Kaake, Robyn M.; Echeverria, Ignacia; Suarez, Marissa; Shamsabadi , Mohammad Karimian; Stoneham, Charlotte; Ramirez, Peter W.; Kress, Jacob; Singh, Rajendra; Sali, Andrej; Krogan , Nevan; Guatelli, John; Jia , Xiaofei

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: DOE - Office Of Science; NIH

OSTI ID:: 1836770

Journal Information:: Nat. Struct. Mol. Biol., Journal Name: Nat. Struct. Mol. Biol. Vol. 27

Country of Publication:: United States

Language:: ENGLISH

References (67)

Structural Basis for Tetherin Antagonism as a Barrier to Zoonotic Lentiviral Transmission Buffalo, Cosmo Z.; Stürzel, Christina M.; Heusinger, Elena Cell Host & Microbe, Vol. 26, Issue 3 https://doi.org/10.1016/j.chom.2019.08.002	journal	September 2019
Cargo Recognition in Clathrin-Mediated Endocytosis Traub, L. M.; Bonifacino, J. S. Cold Spring Harbor Perspectives in Biology, Vol. 5, Issue 11 https://doi.org/10.1101/cshperspect.a016790	journal	November 2013
A Large-Scale Conformational Change Couples Membrane Recruitment to Cargo Binding in the AP2 Clathrin Adaptor Complex Jackson, Lauren P.; Kelly, Bernard T.; McCoy, Airlie J. Cell, Vol. 141, Issue 7 https://doi.org/10.1016/j.cell.2010.05.006	journal	June 2010
Genomic Structure of an Attenuated Quasi Species of HIV-1 from a Blood Transfusion Donor and Recipients Deacon, N. J.; Tsykin, A.; Solomon, A. Science, Vol. 270, Issue 5238 https://doi.org/10.1126/science.270.5238.988	journal	November 1995
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Functional Characterization of the Human Immunodeficiency Virus Type 1 Nef Acidic Domain Baugh, Laura L.; Garcia, J. Victor; Foster, John L. Journal of Virology, Vol. 82, Issue 19 https://doi.org/10.1128/JVI.00107-08	journal	October 2008
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Production of Authentic SARS-CoV Mpro with Enhanced Activity: Application as a Novel Tag-cleavage Endopeptidase for Protein Overproduction Xue, Xiaoyu; Yang, Haitao; Shen, Wei Journal of Molecular Biology, Vol. 366, Issue 3 https://doi.org/10.1016/j.jmb.2006.11.073	journal	February 2007
HIV-1 Nef: Taking Control of Protein Trafficking: Manipulation of Protein Sorting Machinery by HIV-1 Nef Pereira, Estela A.; daSilva, Luis L. P. Traffic, Vol. 17, Issue 9 https://doi.org/10.1111/tra.12412	journal	June 2016
Human immunodeficiency virus type 1 Vpu protein regulates the formation of intracellular gp160-CD4 complexes Willey, R. L.; Maldarelli, F.; Martin, M. A. Journal of Virology, Vol. 66, Issue 1 https://doi.org/10.1128/jvi.66.1.226-234.1992	journal	January 1992
Structural basis of evasion of cellular adaptive immunity by HIV-1 Nef Jia, Xiaofei; Singh, Rajendra; Homann, Stefanie Nature Structural & Molecular Biology, Vol. 19, Issue 7 https://doi.org/10.1038/nsmb.2328	journal	June 2012
Integrative Structural Biology Ward, A. B.; Sali, A.; Wilson, I. A. Science, Vol. 339, Issue 6122 https://doi.org/10.1126/science.1228565	journal	February 2013
Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies Russel, Daniel; Lasker, Keren; Webb, Ben PLoS Biology, Vol. 10, Issue 1 https://doi.org/10.1371/journal.pbio.1001244	journal	January 2012
Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine-lysine distances: Evaluating Lysine-Lysine Distances by MD for XL-MS Merkley, Eric D.; Rysavy, Steven; Kahraman, Abdullah Protein Science, Vol. 23, Issue 6 https://doi.org/10.1002/pro.2458	journal	April 2014
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
Human Immunodeficiency Virus Type 1 Nef Protein Targets CD4 to the Multivesicular Body Pathway daSilva, Luis L. P.; Sougrat, Rachid; Burgos, Patricia V. Journal of Virology, Vol. 83, Issue 13 https://doi.org/10.1128/JVI.00548-09	journal	July 2009
Human immunodeficiency virus type 1 Nef and p56lck protein-tyrosine kinase interact with a common element in CD4 cytoplasmic tail. Salghetti, S.; Mariani, R.; Skowronski, J. Proceedings of the National Academy of Sciences, Vol. 92, Issue 2 https://doi.org/10.1073/pnas.92.2.349	journal	January 1995
Uncertainty in integrative structural modeling Schneidman-Duhovny, Dina; Pellarin, Riccardo; Sali, Andrej Current Opinion in Structural Biology, Vol. 28 https://doi.org/10.1016/j.sbi.2014.08.001	journal	October 2014
Molecular Architecture of the 40S⋅eIF1⋅eIF3 Translation Initiation Complex Erzberger, Jan P.; Stengel, Florian; Pellarin, Riccardo Cell, Vol. 159, Issue 5 https://doi.org/10.1016/j.cell.2014.11.001	journal	November 2014
Developing an Acidic Residue Reactive and Sulfoxide-Containing MS-Cleavable Homobifunctional Cross-Linker for Probing Protein–Protein Interactions Gutierrez, Craig B.; Yu, Clinton; Novitsky, Eric J. Analytical Chemistry, Vol. 88, Issue 16 https://doi.org/10.1021/acs.analchem.6b02240	journal	July 2016
A Basic Patch on α-Adaptin Is Required for Binding of Human Immunodeficiency Virus Type 1 Nef and Cooperative Assembly of a CD4-Nef-AP-2 Complex Chaudhuri, Rittik; Mattera, Rafael; Lindwasser, O. Wolf Journal of Virology, Vol. 83, Issue 6 https://doi.org/10.1128/JVI.02227-08	journal	March 2009
The PRIDE database and related tools and resources in 2019: improving support for quantification data Perez-Riverol, Yasset; Csordas, Attila; Bai, Jingwen Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1106	journal	November 2018
Human immunodeficiency virus types 1 and 2 and simian immunodeficiency virus Nef use distinct but overlapping target sites for downregulation of cell surface CD4 Hua, J.; Cullen, B. R. Journal of Virology, Vol. 71, Issue 9 https://doi.org/10.1128/jvi.71.9.6742-6748.1997	journal	September 1997
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop Sali, Andrej; Berman, Helen M.; Schwede, Torsten Structure, Vol. 23, Issue 7 https://doi.org/10.1016/j.str.2015.05.013	journal	July 2015
Determining the architectures of macromolecular assemblies Alber, Frank; Dokudovskaya, Svetlana; Veenhoff, Liesbeth M. Nature, Vol. 450, Issue 7170 https://doi.org/10.1038/nature06404	journal	November 2007
Endocytic sorting motif interactions involved in Nef-mediated downmodulation of CD4 and CD3 Manrique, Santiago; Sauter, Daniel; Horenkamp, Florian A. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-00481-z	journal	September 2017
Downregulation of CD4 by Human Immunodeficiency Virus Type 1 Nef Is Dependent on Clathrin and Involves Direct Interaction of Nef with the AP2 Clathrin Adaptor Chaudhuri, Rittik; Lindwasser, O. Wolf; Smith, William J. Journal of Virology, Vol. 81, Issue 8 https://doi.org/10.1128/JVI.02725-06	journal	April 2007
HIV F/3' orf encodes a phosphorylated GTP-binding protein resembling an oncogene product Guy, Bruno; Kieny, Marie Paule; Riviere, Yves Nature, Vol. 330, Issue 6145 https://doi.org/10.1038/330266a0	journal	November 1987
Mutation of a Conserved Residue (D123) Required for Oligomerization of Human Immunodeficiency Virus Type 1 Nef Protein Abolishes Interaction with Human Thioesterase and Results in Impairment of Nef Biological Functions Liu, Lang Xia; Heveker, Nikolaus; Fackler, Oliver T. Journal of Virology, Vol. 74, Issue 11 https://doi.org/10.1128/JVI.74.11.5310-5319.2000	journal	June 2000
Serine phosphorylation-independent downregulation of cell-surface CD4 by nef Garcia, J. Victor; Miller, A. Dusty Nature, Vol. 350, Issue 6318 https://doi.org/10.1038/350508a0	journal	April 1991
HIV-1 Nef: a master manipulator of the membrane trafficking machinery mediating immune evasion Pawlak, Emily N.; Dikeakos, Jimmy D. Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1850, Issue 4 https://doi.org/10.1016/j.bbagen.2015.01.003	journal	April 2015
Integrative structure and functional anatomy of a nuclear pore complex Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona Nature, Vol. 555, Issue 7697 https://doi.org/10.1038/nature26003	journal	March 2018
Direct In Vitro Binding of Full-Length Human Immunodeficiency Virus Type 1 Nef Protein to CD4 Cytoplasmic Domain Preusser, Andrea; Briese, Lars; Baur, Andreas S. Journal of Virology, Vol. 75, Issue 8 https://doi.org/10.1128/JVI.75.8.3960-3964.2001	journal	April 2001
Co-localization of HIV-1 Nef with the AP-2 adaptor protein complex correlates with Nef-induced CD4 down-regulation Greenberg, M. E. The EMBO Journal, Vol. 16, Issue 23 https://doi.org/10.1093/emboj/16.23.6964	journal	December 1997
CD4 Glycoprotein Degradation Induced by Human Immunodeficiency Virus Type 1 Vpu Protein Requires the Function of Proteasomes and the Ubiquitin-Conjugating Pathway Schubert, Ulrich; Antón, Luis C.; Bačík, Igor Journal of Virology, Vol. 72, Issue 3 https://doi.org/10.1128/JVI.72.3.2280-2288.1998	journal	March 1998
Nef-Induced CD4 and Major Histocompatibility Complex Class I (MHC-I) Down-Regulation Are Governed by Distinct Determinants: N-Terminal Alpha Helix and Proline Repeat of Nef Selectively Regulate MHC-I Trafficking Mangasarian, Aram; Piguet, Vincent; Wang, Jen-Kuei Journal of Virology, Vol. 73, Issue 3 https://doi.org/10.1128/JVI.73.3.1964-1973.1999	journal	March 1999
The Tyrosine Binding Pocket in the Adaptor Protein 1 (AP-1) μ1 Subunit Is Necessary for Nef to Recruit AP-1 to the Major Histocompatibility Complex Class I Cytoplasmic Tail Wonderlich, Elizabeth R.; Williams, Maya; Collins, Kathleen L. Journal of Biological Chemistry, Vol. 283, Issue 6 https://doi.org/10.1074/jbc.M707760200	journal	February 2008
Comparative Protein Modelling by Satisfaction of Spatial Restraints Šali, Andrej; Blundell, Tom L. Journal of Molecular Biology, Vol. 234, Issue 3 https://doi.org/10.1006/jmbi.1993.1626	journal	December 1993
Replica Monte Carlo Simulation of Spin-Glasses Swendsen, Robert H.; Wang, Jian-Sheng Physical Review Letters, Vol. 57, Issue 21 https://doi.org/10.1103/PhysRevLett.57.2607	journal	November 1986
Importance of the nef gene for maintenance of high virus loads and for development of AIDS Kestier, Harry W.; Ringler, Douglas J.; Mori, Kazuyasu Cell, Vol. 65, Issue 4 https://doi.org/10.1016/0092-8674(91)90097-I	journal	May 1991
Absence of Intact nef Sequences in a Long-Term Survivor with Nonprogressive HIV-1 Infection Kirchhoff, Frank; Greenough, Thomas C.; Brettler, Doreen B. New England Journal of Medicine, Vol. 332, Issue 4 https://doi.org/10.1056/NEJM199501263320405	journal	January 1995
Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach Lasker, K.; Forster, F.; Bohn, S. Proceedings of the National Academy of Sciences, Vol. 109, Issue 5 https://doi.org/10.1073/pnas.1120559109	journal	January 2012
Principles for Integrative Structural Biology Studies Rout, Michael P.; Sali, Andrej Cell, Vol. 177, Issue 6 https://doi.org/10.1016/j.cell.2019.05.016	journal	May 2019
Role of Nef in primate lentiviral immunopathogenesis Kirchhoff, F.; Schindler, M.; Specht, A. Cellular and Molecular Life Sciences, Vol. 65, Issue 17 https://doi.org/10.1007/s00018-008-8094-2	journal	April 2008
WebLogo: A Sequence Logo Generator Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc Genome Research, Vol. 14, Issue 6, p. 1188-1190 https://doi.org/10.1101/gr.849004	journal	May 2004
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
Mutational Analysis of HIV-1 Nef: Identification of Two Mutants That Are Temperature-Sensitive for CD4 Downregulation Aiken, Christopher; Krause, Lisa; Chen, Yen-Liang Virology, Vol. 217, Issue 1 https://doi.org/10.1006/viro.1996.0116	journal	March 1996
Human Immunodeficiency Virus Type 1 Nef Domains Required for Disruption of Major Histocompatibility Complex Class I Trafficking Are Also Necessary for Coprecipitation of Nef with HLA-A2 Williams, Maya; Roeth, Jeremiah F.; Kasper, Matthew R. Journal of Virology, Vol. 79, Issue 1 https://doi.org/10.1128/JVI.79.1.632-636.2005	journal	January 2005
HIV-1 Nef Dimerization Is Required for Nef-Mediated Receptor Downregulation and Viral Replication Poe, Jerrod A.; Smithgall, Thomas E. Journal of Molecular Biology, Vol. 394, Issue 2 https://doi.org/10.1016/j.jmb.2009.09.047	journal	November 2009
How HIV-1 Nef hijacks the AP-2 clathrin adaptor to downregulate CD4 Ren, Xuefeng; Park, Sang Yoon; Bonifacino, Juan S. eLife, Vol. 3 https://doi.org/10.7554/eLife.01754	journal	January 2014
Cell-based Fluorescence Complementation Reveals a Role for HIV-1 Nef Protein Dimerization in AP-2 Adaptor Recruitment and CD4 Co-receptor Down-regulation Shu, Sherry T.; Emert-Sedlak, Lori A.; Smithgall, Thomas E. Journal of Biological Chemistry, Vol. 292, Issue 7 https://doi.org/10.1074/jbc.M116.770016	journal	December 2016
Inhibition of HIV-1 progeny virion release by cell-surface CD4 is relieved by expression of the viral Nef protein Ross, Ted M.; Oran, Alp E.; Cullen, Bryan R. Current Biology, Vol. 9, Issue 12 https://doi.org/10.1016/S0960-9822(99)80283-8	journal	June 1999
Interaction with Cellular CD4 Exposes HIV-1 Envelope Epitopes Targeted by Antibody-Dependent Cell-Mediated Cytotoxicity Veillette, M.; Desormeaux, A.; Medjahed, H. Journal of Virology, Vol. 88, Issue 5 https://doi.org/10.1128/JVI.03230-13	journal	December 2013
Statistical potential for assessment and prediction of protein structures Shen, Min-yi; Sali, Andrej Protein Science, Vol. 15, Issue 11 https://doi.org/10.1110/ps.062416606	journal	November 2006
Shock and kill Deeks, Steven G. Nature, Vol. 487, Issue 7408 https://doi.org/10.1038/487439a	journal	July 2012
Cell-surface expression of CD4 reduces HIV-1 infectivity by blocking Env incorporation in a Nef- and Vpu-inhibitable manner Lama, Juan; Mangasarian, Aram; Trono, Didier Current Biology, Vol. 9, Issue 12 https://doi.org/10.1016/S0960-9822(99)80284-X	journal	June 1999
ProteoWizard: open source software for rapid proteomics tools development Kessner, Darren; Chambers, Matt; Burke, Robert Bioinformatics, Vol. 24, Issue 21 https://doi.org/10.1093/bioinformatics/btn323	journal	July 2008
Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex Shi, Yi; Fernandez-Martinez, Javier; Tjioe, Elina Molecular & Cellular Proteomics, Vol. 13, Issue 11 https://doi.org/10.1074/mcp.M114.041673	journal	August 2014
A New in Vivo Cross-linking Mass Spectrometry Platform to Define Protein–Protein Interactions in Living Cells Kaake, Robyn M.; Wang, Xiaorong; Burke, Anthony Molecular & Cellular Proteomics, Vol. 13, Issue 12 https://doi.org/10.1074/mcp.M114.042630	journal	September 2014
A Simple Method for Automated Equilibration Detection in Molecular Simulations Chodera, John D. Journal of Chemical Theory and Computation, Vol. 12, Issue 4 https://doi.org/10.1021/acs.jctc.5b00784	journal	March 2016
Assessing Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures Viswanath, Shruthi; Chemmama, Ilan E.; Cimermancic, Peter Biophysical Journal, Vol. 113, Issue 11 https://doi.org/10.1016/j.bpj.2017.10.005	journal	December 2017
Downregulation of cell-surface CD4 expression by simian immunodeficiency virus Nef prevents viral super infection. Benson, R. E.; Sanfridson, A.; Ottinger, J. S. Journal of Experimental Medicine, Vol. 177, Issue 6 https://doi.org/10.1084/jem.177.6.1561	journal	June 1993
Structures of Two Coronavirus Main Proteases: Implications for Substrate Binding and Antiviral Drug Design Xue, Xiaoyu; Yu, Hongwei; Yang, Haitao Journal of Virology, Vol. 82, Issue 5 https://doi.org/10.1128/JVI.02114-07	journal	December 2007
Interaction with the Src Homology (SH3-SH2) Region of the Src-family Kinase Hck Structures the HIV-1 Nef Dimer for Kinase Activation and Effector Recruitment Alvarado, John Jeff; Tarafdar, Sreya; Yeh, Joanne I. Journal of Biological Chemistry, Vol. 289, Issue 41 https://doi.org/10.1074/jbc.M114.600031	journal	August 2014
Nef induces CD4 endocytosis: Requirement for a critical dileucine motif in the membrane-proximal CD4 cytoplasmic domain Aiken, Christopher; Konner, Jason; Landau, Nathaniel R. Cell, Vol. 76, Issue 5 https://doi.org/10.1016/0092-8674(94)90360-3	journal	March 1994
Identification of Regions in HIV-1 Nef Required for Efficient Downregulation of Cell Surface CD4 Hua, Jian; Blair, Wade; Truant, Ray Virology, Vol. 231, Issue 2 https://doi.org/10.1006/viro.1997.8517	journal	May 1997

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