5NAY

Crystal structures of homooligomers of collagen type IV. alpha1NC1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of collagen IV globular domains: insight into associated pathologies, folding and network assembly.

Casino, P.Gozalbo-Rovira, R.Rodriguez-Diaz, J.Banerjee, S.Boutaud, A.Rubio, V.Hudson, B.G.Saus, J.Cervera, J.Marina, A.

(2018) IUCrJ 5: 765-779

  • DOI: 10.1107/S2052252518012459
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Basement membranes are extracellular structures of epithelia and endothelia that have collagen IV scaffolds of triple α-chain helical protomers that associate end-to-end, forming networks. The molecular mechanisms by which the noncollagenous C-termin ...

    Basement membranes are extracellular structures of epithelia and endothelia that have collagen IV scaffolds of triple α-chain helical protomers that associate end-to-end, forming networks. The molecular mechanisms by which the noncollagenous C-terminal domains of α-chains direct the selection and assembly of the α1α2α1 and α3α4α5 hetero-oligomers found in vivo remain obscure. Autoantibodies against the noncollagenous domains of the α3α4α5 hexamer or mutations therein cause Goodpasture's or Alport's syndromes, respectively. To gain further insight into oligomer-assembly mechanisms as well as into Goodpasture's and Alport's syndromes, crystal structures of non-collagenous domains produced by recombinant methods were determined. The spontaneous formation of canonical homohexamers (dimers of trimers) of these domains of the α1, α3 and α5 chains was shown and the components of the Goodpasture's disease epitopes were viewed. Crystal structures of the α2 and α4 non-collagenous domains generated by recombinant methods were also determined. These domains spontaneously form homo-oligomers that deviate from the canonical architectures since they have a higher number of subunits (dimers of tetramers and of hexamers, respectively). Six flexible structural motifs largely explain the architectural variations. These findings provide insight into noncollagenous domain folding, while supporting the in vivo operation of extrinsic mechanisms for restricting the self-assembly of noncollagenous domains. Intriguingly, Alport's syndrome missense mutations concentrate within the core that nucleates the folding of the noncollagenous domain, suggesting that this syndrome, when owing to missense changes, is a folding disorder that is potentially amenable to pharmacochaperone therapy.


    Organizational Affiliation

    Microbiology and Biotechnology, Biocenter Klein Flottbek, Ohnhorststr. 18, 22609 Hamburg, Germany.,Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen, DK-2100, Denmark.,Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA. Electronic address: bjorkman@caltech.edu.,Department of Computer Science and Engineering , Texas A&M University , 3112 TAMU , College Station , Texas 77842 , United States.,Department of Chemistry , John Brown University , 2000 West University Street , Siloam Springs , Arkansas 72761 , United States.,From the Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 and hejianhua@sinap.ac.cn.,Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Chemistry and Biochemistry, 103 Chemistry and Biochemistry Building, Montana State University, Bozeman, MT, 59717, USA.,Shandong Provincial Key Laboratory of Synthetic Biology and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Road 189, Qingdao, Shandong 266101, China. cuiqiu@qibebt.ac.cn fengyg@qibebt.ac.cn.,Department of Chemistry and Biochemistry , New Mexico State University , Las Cruces , New Mexico 88003 , United States.,Department of Physics and Astronomy and LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands lp212@cam.ac.uk g.j.l.wuite@vu.nl e.j.g.peterman@vu.nl.,Department of Medicine at Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,CIBER de Enfermedades Raras (CIBERER-ISCIII), Spain.,Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea; Institute of Life Science and Natural Resources, Korea University, Seoul, 02841, Republic of Korea. Electronic address: structures@korea.ac.kr.,Department of Biomedical & Molecular Sciences, Queen's University, Kingston, ON, Canada K7L 3N6.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China; Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Department of Defense, Center for Prostate Disease Research, Bethesda, Maryland, USA.,the Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195.,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.,Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Division of Biotechnology, Advanced Institute of Environment and Bioscience, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 54596, Republic of Korea.,Department of Chemistry and Institute for Molecular Biology and Genetics, Chonbuk National University, Jeonju 54896, Republic of Korea.,Molecular Biology of Microbial Consortia, University of Hamburg, Biocenter Klein Flottbek, Ohnhorststr. 18, 22609, Hamburg, Germany.,Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Department of Chemistry and Biochemistry, 3210 N Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA.,Advanced Photon Technology Division, Research Infrastructure Group, SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: jxqi@im.ac.cn.,Graduate School of Life Sciences, Tohoku University, 2-1-1, Katahira Aoba-ku, Sendai, Miyagi, 980-8577, Japan.,Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA. Electronic address: glander@scripps.edu.,Department of Chemistry , Indiana University , Bloomington , Indiana 47405-7102 United States.,Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen, DK-2100, Denmark. Electronic address: leila@chem.ku.dk.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA. Electronic address: bwiedenheft@gmail.com.,Department of Chemistry , Texas A&M University , P.O. Box 30012, College Station , Texas 77842 , United States.,Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China. Electronic address: mikyeken@dlnu.edu.cn.,School of Life Science and Biotechnology, Dalian University of Technology, No 2 Linggong Road, Dalian, 116024, Liaoning, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.,Department of Cell and Molecular Biology, Grand Valley State University , Allendale, Michigan 49401, United States.,Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden. Electronic address: stenmark@dbb.su.se.,South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France.,Istituto di Biofisica , Consiglio Nazionale delle Ricerche , 56124 Pisa , Italy.,Department of Agricultural Biotechnology, Seoul National University, 1 Gwanak-ro, Seoul 08826, Republic of Korea.,Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States.,Department of Chemistry , King's College London , 7 Trinity Street , London SE1 1DB , U.K.,Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA.,Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-IPN, Ciudad de México, Mexico.,the Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan.,Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Department of Biochemistry and Molecular Biology/ERI BIOTECMED, Universitat de València, Dr Moliner 50, Burjassot, 46100 Valencia, Spain.,Graduate Program in Biophysics, Harvard University, Cambridge, MA, 02138, USA.,Department of Chemistry, University of California Berkeley, Berkeley, CA, 94720, USA.,Dipartimento di Scienze Chimiche , Università degli Studi di Padova and Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche , 35131 Padua , Italy.,Division of Cardiovascular Medicine, Department of Internal Medicine, Center for Arrhythmia Research, University of Michigan, Ann Arbor, MI, United States.,Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China.,Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, United States.,Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: wenty@im.ac.cn.,RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. takuhiro.ito@riken.jp.,Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Agricultural Chemistry, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan. Electronic address: sue@nodai.ac.jp.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.,b Interdisciplinary Research Center on Biology and Chemistry , Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , Shanghai , China.,Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, 94720, USA.,Department of Integrative Oncology , BC Cancer Research Centre , V5Z 1L3 Vancouver Vancouver , British Columbia , Canada.,Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany.,Structural Biology Research Center (SBRC), Institute of Materials Structure Science (IMSS), High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.,Max Delbrück Center for Molecular Medicine, Kristallographie, Robert-Rössle-Strasse 10, Berlin, 13125, Germany.,Winkle College of Pharmacy, University of Cincinnati, ML 0514, 231 Albert Sabin Way, MSB 3109B, Cincinnati, OH, 45267, USA.,Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France. almouzni@curie.fr.,Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, Collaborative Innovation Center of Chemistry for Life Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China.,Burnett School of Biomedical Sciences, College of Medicine , University of Central Florida , Orlando , Florida 32827 , United States.,Department of Physiology, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile.,Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milan, Italy.,Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15260.,From the Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 and yufeng@sinap.ac.cn.,The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York NY 10027, USA.,From the Department of Biochemistry, s-nair@life.illinois.edu.,Munich Center for Integrated Protein Science, 81377 München, Germany.,From the Bioconversion Group and inoue-h@aist.go.jp.,Department of Molecular Biosciences, 1200 Sunnyside Ave, University of Kansas, Lawrence, KS, 66045, USA.,Department of Biochemistry and Molecular Biology, School of Medicine , Oregon Health & Science University , Portland , Oregon 97239 , United States.,Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden; Science for Life Laboratory Stockholm University, Box 1031, SE-171 21 Solna, Sweden. Electronic address: gunnar@dbb.su.se.,College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea. swkimmd@snu.ac.kr.,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia. mhinds@unimelb.edu.au.,From the Bioconversion Group and.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia. m.kvansakul@latrobe.edu.au.,Department of Life Sciences, Imperial College, London, SW7 2AZ, UK.,Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA.,Inositol Signaling Group, Signal Transduction Laboratory , National Institute of Environmental Health Sciences , Research Triangle Park , North Carolina 27709 , United States.,Dipartimento di Medicina e Chirurgia , Università di Parma , 43125 Parma , Italy.,Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China; School of Life Science and Biotechnology, Dalian University of Technology, No 2 Linggong Road, Dalian, 116024, Liaoning, China.,Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 6997801 Ramat Aviv, Israel.,Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, 100084 Beijing, China; liu_xy@mail.tsinghua.edu.cn bshoichet@gmail.com kobilka@stanford.edu peter.gmeiner@fau.de.,Cancer institute, the Affiliated Hospital of Qingdao University, Qingdao Cancer Institute and School of Basic Medicine, Qingdao University, 266021, Qingdao, China.,Institute for Genomic Biology, and.,Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies (Soken-dai), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.,The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom.,Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158.,Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA.,BioStratum Inc., Durham, North Carolina, USA.,Dipartimento di Scienze degli Alimenti e del Farmaco , Università di Parma , 43124 Parma , Italy.,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5G 1L6, Canada.,a State Key Laboratory of Bioorganic and Natural Products Chemistry , Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , Shanghai , China.,Department of Chemistry, Grand Valley State University , Allendale, Michigan 49401, United States.,University of Florence , Department of Chemistry "Ugo Schiff" , Via della Lastruccia 3 , 50019 Sesto Fiorentino ( Florence ), Italy.,Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada.,Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea.,Biozentrum, University of Basel, 4056 Basel, Switzerland.,Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, 041 54 Košice, Slovakia.,Sorbonne Université, Institut Curie, CNRS, UMR3664, F-75005, Paris, France. almouzni@curie.fr.,CKD Research Institute, Chong Kun Dang Pharmaceutical Corporation, Yongin, 16995, Republic of Korea.,Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, 100084 Beijing, China.,JAN Scientific Inc., Seattle, WA 98105.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia.,Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China.,Division of Respirology, Department of Medicine, Queen's University, Kingston, ON, Canada K7L 3N6.,Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260.,Department of Physics and Astronomy and LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.,Institute of Health Sciences, Shanghai Institutes for Biological Sciences of Chinese Academy of Sciences and Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Mexico.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India. suguna@iisc.ac.in.,Physik Department E22, Technische Universität München, 85748 Garching, Germany.,Department of Biochemistry and Biophysics , Texas A&M University , 3112 TAMU , College Station , Texas 77842 , United States.,From the Department of Biochemistry.,Children's Health Research Institute, Lawson Health Research Institute, 800 Commissioner's Road East, London, ON, N6C 2V5, Canada. sli@uwo.ca.,College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea.,College of Pharmacy, Pusan National University, Busandaehak-ro, Pusan 46241, Republic of Korea.,State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Laboratorio de Reconocimiento Molecular, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, 46012 Valencia, Spain.,Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico.,Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada.,the Polymer Chemistry Group, Research Institute for Sustainable Chemistry, AIST, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan, and.,Departamento de Bioquímica y Biología Molecular at Facultad de Medicina y Odontología, Universitat de València, Blasco Ibáñez 15-17, 46010 Valencia, Spain.,Center for Integrative Proteomics, Rutgers University, Piscataway, NJ 08854, USA.,Department of Biochemistry and Biophysics, Graduate Group in Biochemistry and Molecular Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.,Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark.,Center for Computational Quantum Chemistry, Department of Chemistry , University of Georgia , 140 Cedar Street , Athens , Georgia 30602-2556 , United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158; liu_xy@mail.tsinghua.edu.cn bshoichet@gmail.com kobilka@stanford.edu peter.gmeiner@fau.de.,Department of Physics, University of Oxford, Oxford OX1 3PU, UK.,d Department of Cell Biology , Harvard Medical School , Boston , MA , USA.,Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801 and.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.,Department of Molecular Biosciences, 1200 Sunnyside Ave, University of Kansas, Lawrence, KS, 66045, USA. Electronic address: lamb@ku.edu.,Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China.,Structural Molecular Biology, Stanford Synchroton Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.,Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305.,Integrated Program in Neuroscience, McGill University, Montréal, QC H3A 2B4, Canada; Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada.,Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.,the Bio-based Materials Chemistry Group, Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan.,Department of Biochemistry, University of Cambridge, Cambridge, UK.,Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK.,Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA.,Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260; acohen@slac.stanford.edu guc9@pitt.edu.,Istituto Nazionale Biostrutture e Biosistemi , 00136 Rome , Italy.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China; Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Shilongshan Road No. 18, Xihu District, Hangzhou 310064, Zhejiang Province, China. Electronic address: shi-lab@tsinghua.edu.cn.,Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK; Department of Physiology, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile.,Centro di Biologia Integrata - CIBIO , Università di Trento , 38123 Povo , Trento , Italy.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Departments of Biochemistry and Molecular Genetics, MaRS Centre, West Tower, Floor 16, Toronto, ON, M5G 1M1, Canada.,Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada. Electronic address: derek.bowie@mcgill.ca.,Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China. Electronic address: yongbinxu@dlnu.edu.cn.,Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA.,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.,Laboratory of Molecular Immunology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.,Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , Indiana 47405 United States.,Sorbonne Université, Institut Curie, CNRS, UMR3664, F-75005, Paris, France.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA.,University of Florence , NEUROFARBA Dept., Sezione di Scienze Farmaceutiche , Via Ugo Schiff 6 , 50019 Sesto Fiorentino ( Florence ), Italy.,Department of Life Sciences, Imperial College, London, SW7 2AZ, UK. h.low@imperial.ac.uk.,Department of Pharmaceutical Sciences, University of Connecticut , 69 North Eagleville Road, Storrs, Connecticut 06269, United States.,Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul, 08826, Republic of Korea.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada.,c Collaborative Innovation Center of Chemistry for Life Sciences , Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai , China.,Department of Pharmacology and Physiology , Saint Louis University School of Medicine , M370, Schwitalla Hall, 1402 South Grand Boulevard , Saint Louis , Missouri 63104 , United States.,Physik Department E22, Technische Universität München, 85748 Garching, Germany; mrief@ph.tum.de gabriel.zoldak@upjs.sk.,Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,the University of Chinese Academy of Sciences, Beijing 100049, China.,NAICONS Srl., 20139 Milan, Italy.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.,RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, United States.,Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260.,Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA.,Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany; liu_xy@mail.tsinghua.edu.cn bshoichet@gmail.com kobilka@stanford.edu peter.gmeiner@fau.de.,Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA 92093.,Departamento de Microbiología, Facultad de Medicina at Universitat de València, Blasco Ibáñez 17, 46010 Valencia, Spain.,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea. bwhan@snu.ac.kr.,Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States.,State Key Laboratory of Microbial Metabolism, Shanghai Jiao-Tong University, Shanghai, China.,Rega Institute and Department of Microbiology and Immunology, KU Leuven, 3000 Leuven, Belgium. Electronic address: kalyan.das@kuleuven.be.,Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, United States.,Department of Biochemistry, University of Cambridge, Cambridge, UK lp212@cam.ac.uk g.j.l.wuite@vu.nl e.j.g.peterman@vu.nl.,Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA. Electronic address: ebright@waksman.rutgers.edu.,Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada. sli@uwo.ca.,Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany.,Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Jaume Roig 11, 46010 Valencia, Spain.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.,Department of Neurology, Chonbuk National University School of Medicine, Jeonju 54896, Republic of Korea.,From the Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 and.,Structural Molecular Biology, Stanford Synchroton Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025; acohen@slac.stanford.edu guc9@pitt.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Collagen alpha-1(IV) chain
A, B, C, D, E, F
229Homo sapiensMutation(s): 0 
Gene Names: COL4A1
Find proteins for P02462 (Homo sapiens)
Go to Gene View: COL4A1
Go to UniProtKB:  P02462
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 94.851α = 90.00
b = 127.045β = 90.00
c = 130.543γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHASERphasing
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-02-28 
  • Released Date: 2018-09-12 
  • Deposition Author(s): Casino, P., Marina, A.

Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBIO2013-42619-P
Spanish Ministry of Economy and CompetitivenessSpainBFU2016-78606-P

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Database references
  • Version 1.2: 2018-11-28
    Type: Data collection, Database references