6BEH

Crystal structure of VACV D13 in complex with Rifapentine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural basis for the inhibition of poxvirus assembly by the antibiotic rifampicin.

Garriga, D.Headey, S.Accurso, C.Gunzburg, M.Scanlon, M.Coulibaly, F.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 8424-8429

  • DOI: 10.1073/pnas.1810398115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Poxviruses are large DNA viruses that cause disease in animals and humans. They differ from classical enveloped viruses, because their membrane is acquired from cytoplasmic membrane precursors assembled onto a viral protein scaffold formed by the D13 ...

    Poxviruses are large DNA viruses that cause disease in animals and humans. They differ from classical enveloped viruses, because their membrane is acquired from cytoplasmic membrane precursors assembled onto a viral protein scaffold formed by the D13 protein rather than budding through cellular compartments. It was found three decades ago that the antibiotic rifampicin blocks this process and prevents scaffold formation. To elucidate the mechanism of action of rifampicin, we have determined the crystal structures of six D13-rifamycin complexes. These structures reveal that rifamycin compounds bind to a phenylalanine-rich region, or F-ring, at the membrane-proximal opening of the central channel of the D13 trimer. We show by NMR, surface plasmon resonance (SPR), and site-directed mutagenesis that A17, a membrane-associated viral protein, mediates the recruitment of the D13 scaffold by also binding to the F-ring. This interaction is the target of rifampicin, which prevents A17 binding, explaining the inhibition of viral morphogenesis. The F-ring of D13 is both conserved in sequence in mammalian poxviruses and essential for interaction with A17, defining a target for the development of assembly inhibitors. The model of the A17-D13 interaction describes a two-component system for remodeling nascent membranes that may be conserved in other large and giant DNA viruses.


    Organizational Affiliation

    School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland.,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.,School of Medicine, Deakin University, Geelong, VIC 3217, Australia.,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.,High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India.,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.,Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Medical Neurobiology, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China. wywen@fudan.edu.cn.,Department of Chemistry, York Structural Biology Laboratory , University of York , Heslington, York YO10 5DD , United Kingdom.,Department of Experimental Medical Science, Lund University, Lund, Sweden.,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 Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea.,Protein Diffraction Group, Experimental Facility Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan.,Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.,Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, and.,Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Cracow, Poland.,CNRS, IMoPA, Université de Lorraine, Nancy, F-54000, France. xavier.manival@univ-lorraine.fr.,Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Kumamoto 862-0973, Japan; Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto 862-0973, Japan.,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.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.,Depertment of Biochemistry, Faculty of Medicine, Osaka Medical College, Osaka, Japan.,Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation.,Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea. jsunkim@chonnam.ac.kr.,Department of Molecular Genetics, German Institute of Human Nutrition, Potsdam-Rehbruecke, Arthur-Scheunert-Allee, Nuthetal, Germany.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland. Electronic address: allain@mol.biol.ethz.ch.,Faculty of Chemistry, Jagiellonian University, 30-387 Cracow, Poland.,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.,Institute of Biostructures and Bioimaging (IBB), National Research Council & Interuniversity Research Centre on Bioactive Peptides (CIRPEB), Via Mezzocannone 16, 80134 Naples, Italy. Electronic address: marilisa.leone@cnr.it.,Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Medical Neurobiology, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,Hybrigenics Services, Paris, 75014, France.,From the Departments of Antibody Discovery and Protein Engineering.,Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany.,IGF, CNRS, Université de Montpellier, Montpellier, 34090, 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.,Department of Chemical and Biological Engineering; University of Wisconsin-Madison; 1415 Engineering Drive; Madison, WI, 53706.,Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, Via Argine 1085, 80147 Naples, Italy.,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.,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.,Temasek Life Sciences Laboratory, Department of Biological Sciences, National University of Singapore, Singapore, 117604, Singapore. caiyu@tll.org.sg.,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.,CNRS, IMoPA, Université de Lorraine, Nancy, F-54000, France.,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.,Graduate School of Science, Osaka City University, Osaka, Japan.,Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105.,From the Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104 augen-pioszak@ouhsc.edu.,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.,BioBank, First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Shaanxi Sheng 710061, China.,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.,Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania. Electronic address: matulis@ibt.lt.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.,IGMM, CNRS, Université de Montpellier, Montpellier, 34293, France. edouard.bertrand@igmm.cnrs.fr.,ED515, Paris Sorbonne Université, 75006 Paris, France.,Department of Biological Sciences, University of Bergen, Thormøhlens gate 53, Bergen, 5006, Norway.,Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia.,Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines , McGill University , Montreal , QC H3G 0B1 , Canada.,College of Pharmaceutical Sciences , Zhejiang University of Technology , Hangzhou 310014 , P. R. China.,iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal.,From the Departments of Antibody Discovery and Protein Engineering, dallacquaw@medimmune.com.,CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Departments of Chemistry and Global Health , University of Washington , 36 Bagley Hall, 400 15th Avenue NE , Seattle , Washington 98195 , United States.,From the Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104.,Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Kumamoto 862-0973, Japan.,Institute for Frontier Materials, Deakin University, Geelong, VIC 3217, Australia.,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.,Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, Hofackerstrasses 30, 4132 Muttenz, Switzerland. Electronic address: georg.lipps@fhnw.ch.,the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025.,The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, Tromsø, 9037, Norway.,Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, SW7 2AZ London, United Kingdom; s.j.matthews@imperial.ac.uk s.r.wig@imperial.ac.uk.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia.,Institute for Protein Design, University of Washington, Seattle, WA, USA.,Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, and eddjames@soton.ac.uk.,Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania.,From the Departments of Antibody Discovery and Protein Engineering, oganesyanv@medimmune.com.,Unité Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528, CNRS, 75015 Paris, France.,the Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom.,Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan.,State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China.,CRBM, University of Montpellier, CNRS, 1919 Route de Mende, Montpellier, 34090, France.,College of Medicine, Kyungpook National University, Daegu, 41940, Republic of Korea.,Biosuperiors, MedImmune, Gaithersburg, Maryland 20878.,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.,Firebird Biomolecular Sciences LLC, Alachua, FL 32615, USA.,Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.,Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York.,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.,Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.,Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA. Electronic address: snowren@berkeley.edu.,Temasek Life Sciences Laboratory, Department of Biological Sciences, National University of Singapore, Singapore, 117604, Singapore.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States.,Department of Microbiology & Immunology , Columbia University Irving Medical Center , 701 West 168th Street, HHSC 1502 , New York , New York 10032 , United States.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.,Division of Infectious Diseases, Department of Medicine , Columbia University Irving Medical Center , PH8-W, 630 West 168th Street, PH 8-West , New York , New York 10032 , United States.,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.,California NanoSystems Institute, University of California at Los Angeles, Los Angeles, California.,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 Protein - DNA Interactions, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania.,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.,Uni Research, Center for Applied Biotechnology, Thormøhlens gate 55, Bergen, 5006, Norway.,Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, SW7 2AZ London, United Kingdom.,Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan.,Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York. Electronic address: rad82@cornell.edu.,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 Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,Institute of Biophysics, Consiglio Nazionale delle Ricerche, Genova, Italy.,Institute of Biostructures and Bioimaging (IBB), National Research Council & Interuniversity Research Centre on Bioactive Peptides (CIRPEB), Via Mezzocannone 16, 80134 Naples, Italy.,Experimental Molecular Biophysics, Institute of Physics, Freie Universität Berlin, 14195 Berlin, Germany.,Equipe labélisée Ligue Nationale Contre le Cancer, 34293, Montpellier, France. edouard.bertrand@igmm.cnrs.fr.,Faculty of Chemistry and Chemical Technology , University of Ljubljana , Večna pot 113 , SI-1000 Ljubljana , Slovenia.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.,Department of Herbal Medicine Resources, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 54596, Republic of Korea.,Equipe labélisée Ligue Nationale Contre le Cancer, 34293, Montpellier, France.,Department of Biochemistry , University of Texas Southwestern Medical Center , 5323 Harry Hines Blvd , Dallas , Texas 75390 , United States.,Department of Biophysics , University of Texas Southwestern Medical Center , 5323 Harry Hines Blvd , Dallas , Texas 75390 , United States.,Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan.,Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan.,Pohang Accelerator Laboratory, Pohang, Gyeongbuk, 37673, Republic of Korea.,Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: jimhurley@berkeley.edu.,INRA, CNRS, Centre des Sciences du Goût et de l'Alimentation, Université de Bourgogne-Franche Comté, Dijon, France.,From the Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland. Electronic address: boudet.julien@gmail.com.,The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, CB2 0XY Cambridge, United Kingdom.,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.,Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan. Electronic address: hira@life.sojo-u.ac.jp.,Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Department of Biochemistry, University of Oxford, Oxford, UK.,From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil.,Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, Hofackerstrasses 30, 4132 Muttenz, Switzerland.,CNRS, INSERM, IBSLOR, Université de Lorraine, Nancy, F-54000, France.,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.,Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States.,Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States.,a Department of Biotherapeutic and Medicinal Sciences , Biogen , Cambridge , MA , USA.,Department of Computer Science, Genome Center, University of California, Davis, CA 94520.,Slovenian NMR Center , National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,Amazon, Seattle, WA, USA.,Centre for Cancer Immunology, University of Southampton Faculty of Medicine, University Hospital Southampton, Southampton SO16 6YD, United Kingdom.,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.,Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics' of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation.,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.,Unité Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528, CNRS, 75015 Paris, France; marc.delarue@pasteur.fr.,Department of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan.,Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, 67000, France.,Analytical Sciences, and.,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.,IGMM, CNRS, Université de Montpellier, Montpellier, 34293, France.,Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC 3052, Australia.,Department of Pathology, Amsterdam Neuroscience, VU University Medical Center, de Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.,Institute for Protein Design, University of Washington, Seattle, WA, USA. dabaker@uw.edu.,Vollum Institute, Oregon Health and Science University, Portland, United States.,Unité Récepteurs-Canaux, Institut Pasteur, UMR 3571, CNRS, 75015 Paris, France.,the Laboratório Nacional de Nanotecnologia, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia; Fasseli.Coulibaly@monash.edu.,School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , P. R. China.,Biomedical Manufacturing, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia.,Department of Chemical Engineering; Pennsylvania State University; 158 Fenske Laboratory; University Park, PA, 16802.,University of Florence, NEUROFARBA Department, Sezione di Farmaceutica e Nutraceutica, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy.,School of Biomedical Sciences, Chung Shan Medical University, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, No.110, Sec.1, Chien-Kuo N. Rd, Taichung City, Taiwan. Electronic address: cyhuang@csmu.edu.tw.,SOLEIL Synchrotron, L'Orme de Merisiers, Saint-Aubin, Gif-sur-Yvette, France.,Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.,Parasites and Microbes Programme , Wellcome Sanger Institute , Hinxton, Cambridgeshire CB10 1SA , U.K.,Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.,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.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal.,Department of Biochemistry & Molecular Biology, Oregon Health and Science University, Portland, United States.,Department of Computer Science, University of California, Santa Cruz, Santa Cruz, CA, USA.,The OCU Advanced Research Institute for Natural Science and Technology, Osaka City University, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Scaffold protein D13
A, B, C
553Vaccinia virus (strain Western Reserve)Mutation(s): 0 
Find proteins for P68440 (Vaccinia virus (strain Western Reserve))
Go to UniProtKB:  P68440
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B, C
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
RPT
Query on RPT

Download SDF File 
Download CCD File 
A
RIFAPENTINE
(2R,16S,17R,18R,19R,20S,21S,22S,23S)-8-{[(4-CYCLOPENTYLPIPERAZIN-1-YL)IMINO]METHYL}-5,6,9,17,19-PENTAHYDROXY-23-METHOXY-2,4,12,16,18,20,22-HEPTAMETHYL-1,11-DIOXO-1,2-DIHYDRO-2,7-(EPOXYPENTADECA[1,11,13]TRIENOIMINO)NAPHTHO[2,1-B]FURAN-21-YL ACETATE; 3-(((4-CYCLOPENTYL-1-PIPERAZINYL)IMINO)METHYL)RIFAMYCIN
C47 H64 N4 O12
WDZCUPBHRAEYDL-GZAUEHORSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.198 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 190.790α = 90.00
b = 190.790β = 90.00
c = 253.530γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
BUSTERphasing
Cootmodel building
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (Australia)AustraliaAPP1051907

Revision History 

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2018-08-01
    Type: Data collection, Database references
  • Version 1.2: 2018-08-15
    Type: Data collection, Database references
  • Version 1.3: 2018-08-22
    Type: Data collection, Database references
  • Version 1.4: 2019-02-20
    Type: Author supporting evidence, Data collection