5KZA

Crystal structure of the Rous sarcoma virus matrix protein (aa 2-102). Space group I41


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cholesterol Promotes Protein Binding by Affecting Membrane Electrostatics and Solvation Properties.

Doktorova, M.Heberle, F.A.Kingston, R.L.Khelashvili, G.Cuendet, M.A.Wen, Y.Katsaras, J.Feigenson, G.W.Vogt, V.M.Dick, R.A.

(2017) Biophys. J. 113: 2004-2015

  • DOI: 10.1016/j.bpj.2017.08.055
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Binding of the retroviral structural protein Gag to the cellular plasma membrane is mediated by the protein's matrix (MA) domain. Prominent among MA-PM interactions is electrostatic attraction between the positively charged MA domain and the negative ...

    Binding of the retroviral structural protein Gag to the cellular plasma membrane is mediated by the protein's matrix (MA) domain. Prominent among MA-PM interactions is electrostatic attraction between the positively charged MA domain and the negatively charged plasma membrane inner leaflet. Previously, we reported that membrane association of HIV-1 Gag, as well as purified Rous sarcoma virus (RSV) MA and Gag, depends strongly on the presence of acidic lipids and is enhanced by cholesterol (Chol). The mechanism underlying this enhancement was unclear. Here, using a broad set of in vitro and in silico techniques we addressed molecular mechanisms of association between RSV MA and model membranes, and investigated how Chol enhances this association. In neutron scattering experiments with liposomes in the presence or absence of Chol, MA preferentially interacted with preexisting POPS-rich clusters formed by nonideal lipid mixing, binding peripherally to the lipid headgroups with minimal perturbation to the bilayer structure. Molecular dynamics simulations showed a stronger MA-bilayer interaction in the presence of Chol, and a large Chol-driven increase in lipid packing and membrane surface charge density. Although in vitro MA-liposome association is influenced by disparate variables, including ionic strength and concentrations of Chol and charged lipids, continuum electrostatic theory revealed an underlying dependence on membrane surface potential. Together, these results conclusively show that Chol affects RSV MA-membrane association by making the electrostatic potential at the membrane surface more negative, while decreasing the penalty for lipid headgroup desolvation. The presented approach can be applied to other viral and nonviral proteins.


    Organizational Affiliation

    School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud and Université Paris-Saclay, Gif-sur-Yvette, France.,Department of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States.,Institute for Protein Design, University of Washington, Seattle, WA, USA. emarcos82@gmail.com.,Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390.,From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil, sandra.dias@lnbio.cnpem.br.,High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India.,California NanoSystems Institute, University of California at Los Angeles, Los Angeles, California.,Department of Life Sciences, National Central University, Taoyuan, 32001, Taiwan. chinyuchen@cc.ncu.edu.tw.,From the Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 and William.Royer@umassmed.edu.,Food Technology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India.,Infinitus (China) Co. Ltd. , Guangzhou 510663 , P. R. China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Department of Experimental Medical Science, Lund University, Lund, Sweden.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China. Electronic address: jtzheng@sjtu.edu.cn.,Department of Applied Biology and Chemical Technology, Central Laboratory of Institute of Molecular Technology for Drug Discovery and Synthesis, The Hong Kong Polytechnic University, Hung Hom, Hong Hong, China.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York.,Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York. Electronic address: rad82@cornell.edu.,Protein Diffraction Group, Experimental Facility Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.,Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,From the Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 and.,the Carlson School of Chemistry and Biochemistry, Clark University, Worcester, Massachusetts 01610.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Institute of Biophysics, Consiglio Nazionale delle Ricerche, Genova, Italy.,Department of Life Sciences, National Central University, Taoyuan, 32001, Taiwan.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London, United Kingdom.,Department of Biochemistry, University of Washington, Seattle, WA, USA. emarcos82@gmail.com.,Faculty of Chemistry and Chemical Technology , University of Ljubljana , Večna pot 113 , SI-1000 Ljubljana , Slovenia.,Department of Herbal Medicine Resources, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 54596, Republic of Korea.,Department of Molecular Genetics, German Institute of Human Nutrition, Potsdam-Rehbruecke, Arthur-Scheunert-Allee, Nuthetal, Germany.,Foundation for Applied Molecular Evolution and the Westheimer Institute of Science & Technology, Alachua, FL 32615, USA.,Ingénierie Moléculaire et Physiopathologie Articulaire, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7365, Université de Lorraine, Biopôle de l'Université de Lorraine, Vandoeuvre-les-Nancy Cedex, France.,Department of Biochemistry, University of Washington, Seattle, WA, USA.,Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan.,INRA, CNRS, Centre des Sciences du Goût et de l'Alimentation, Université de Bourgogne-Franche Comté, Dijon, France.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands.,School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261.,The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, CB2 0XY Cambridge, United Kingdom.,Department of Chemical and Biological Engineering; University of Wisconsin-Madison; 1415 Engineering Drive; Madison, WI, 53706.,GM/CA, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: wilson@scripps.edu.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390; dan.rosenbaum@utsouthwestern.edu.,The Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, CB2 0QH Cambridge, United Kingdom.,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.,MRC Laboratory of Molecular Biology, Cambridge, UK. jyl@mrc-lmb.cam.ac.,From the Departments of Structural Biology and.,MRC Laboratory of Molecular Biology, Cambridge, UK.,Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York.,Institute of Biochemistry, Graz University of Technology, Graz, Austria.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, Oulu, Finland.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands; Department of Neurology, Amsterdam Neuroscience, Academic Medical Center, Meidreefberg 9, 1105 AZ Amsterdam, the Netherlands; Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA.,Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, 3210 Merryfield Row, San Diego, CA 92121, USA.,School of Biochemistry, Devi Ahilya University, Indore, India.,Department of Biochemistry, University of Oxford, Oxford, UK.,Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105.,From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil.,Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom.,Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, California.,From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil, andre.ambrosio@lnbio.cnpem.br.,Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain. emarcos82@gmail.com.,Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom.,Cyrus Biotechnology, Seattle, WA, USA.,Department of Biochemistry; University of Wisconsin-Madison; 440 Henry Mall; Madison, WI, 53706.,Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States.,College of Pharmaceutical Sciences , Zhejiang University of Technology , Hangzhou 310014 , P. R. China.,Slovenian NMR Center , National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,Amazon, Seattle, WA, USA.,CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, CB2 0XY Cambridge, United Kingdom; walker@mrc-mbu.cam.ac.uk.,MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.,EN-FIST Center of Excellence , Trg OF 13 , SI-1000 Ljubljana , Slovenia.,Department of Microbiology, Immunology & Molecular Genetics, University of California at Los Angeles, Los Angeles, California.,Department of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan.,Department of Chemistry, Umeå University, Umeå, Sweden.,Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Department of Biochemistry, University of Washington, Seattle, WA, USA. dabaker@uw.edu.,the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025.,Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry , University of California, Irvine , Irvine , California 92697-3900 , United States.,Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA.,Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.,Institute for Protein Design, University of Washington, Seattle, WA, USA.,Department of Pathology, Amsterdam Neuroscience, VU University Medical Center, de Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.,the Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom.,Institute for Protein Design, University of Washington, Seattle, WA, USA. dabaker@uw.edu.,Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan.,the Laboratório Nacional de Nanotecnologia, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil.,the School of Electrical and Computer Engineering, University of Campinas, São Paulo 13083-852, Brazil, and.,Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105 charles.rock@stjude.org.,School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , P. R. China.,Firebird Biomolecular Sciences LLC, Alachua, FL 32615, USA.,Department of Chemical Engineering; Pennsylvania State University; 158 Fenske Laboratory; University Park, PA, 16802.,SOLEIL Synchrotron, L'Orme de Merisiers, Saint-Aubin, Gif-sur-Yvette, France.,Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.,Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.,Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China.,The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee.,Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.,Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom.,The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee. Electronic address: heberlefa@ornl.gov.,Department of Microbiology and Immunology, University of Otago, 9016 Dunedin, New Zealand.,Department of Computer Science, University of California, Santa Cruz, Santa Cruz, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
virus matrix protein
A
104Rous sarcoma virus (strain Prague C)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P03354 (Rous sarcoma virus (strain Prague C))
Go to UniProtKB:  P03354
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.164 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 79.000α = 90.00
b = 79.000β = 90.00
c = 27.800γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Health Research Council (HRC)New Zealand--

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2019-02-06
    Type: Data collection, Database references
  • Version 1.2: 2020-01-01
    Type: Author supporting evidence