6MFG

HLA-DQ2-glia-alpha1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discriminative T-cell receptor recognition of highly homologous HLA-DQ2-bound gluten epitopes.

Dahal-Koirala, S.Ciacchi, L.Petersen, J.Risnes, L.F.Neumann, R.S.Christophersen, A.Lundin, K.E.A.Reid, H.H.Qiao, S.W.Rossjohn, J.Sollid, L.M.

(2019) J. Biol. Chem. 294: 941-952

  • DOI: 10.1074/jbc.RA118.005736
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Celiac disease (CeD) provides an opportunity to study the specificity underlying human T-cell responses to an array of similar epitopes presented by the same human leukocyte antigen II (HLA-II) molecule. Here, we investigated T-cell responses to the ...

    Celiac disease (CeD) provides an opportunity to study the specificity underlying human T-cell responses to an array of similar epitopes presented by the same human leukocyte antigen II (HLA-II) molecule. Here, we investigated T-cell responses to the two immunodominant and highly homologous HLA-DQ2.5-restricted gluten epitopes, DQ2.5-glia-α1a (PFPQPELPY) and DQ2.5-glia-ω1 (PFPQPEQPF). Using HLA-DQ2.5-DQ2.5-glia-α1a and HLA-DQ2.5-DQ2.5-glia-ω1 tetramers and single-cell αβ T-cell receptor (TCR) sequencing, we observed that despite similarity in biased variable-gene usage in the TCR repertoire responding to these nearly identical peptide-HLA-II complexes, most of the T cells are specific for either of the two epitopes. To understand the molecular basis of this exquisite fine specificity, we undertook Ala substitution assays revealing that the p7 residue (Leu/Gln) is critical for specific epitope recognition by both DQ2.5-glia-α1a- and DQ2.5-glia-ω1-reactive T-cell clones. We determined high-resolution binary crystal structures of HLA-DQ2.5 bound to DQ2.5-glia-α1a (2.0 Å) and DQ2.5-glia-ω1 (2.6 Å). These structures disclosed that differences around the p7 residue subtly alter the neighboring substructure and electrostatic properties of the HLA-DQ2.5-peptide complex, providing the fine specificity underlying the responses against these two highly homologous gluten epitopes. This study underscores the ability of TCRs to recognize subtle differences in the peptide-HLA-II landscape in a human disease setting.


    Organizational Affiliation

    School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Molecular Partners AG, Wagistrasse 14, 8952, Schlieren, Switzerland. info@molecularpartners.com.,Medicinal Chemistry & Drug Discovery, Department of Pharmacology , University of Oxford , Mansfield Road , Oxford OX1 3QT , U.K.,Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand.,Experimental Therapeutics Centre, Agency for Science, Technology and Research (A(∗)STAR), 31 Biopolis way, Nanos, #03-01, Singapore 138669, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore. Electronic address: knacro@etc.a-star.edu.sg.,Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy; Department of Mechanistic Cell Biology, Max-Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany.,Ipsen Bioinnovation, 102 Park Drive, Milton Park, Abingdon OX14 4RY, UK.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, 450 Vojvode Stepe, 11000, Belgrade, Serbia.,Neuprozyme Therapeutics A/S, 2970 Hörsholm, Denmark. Electronic address: jp@neuprozyme.com.,SARomics Biostructures, 223 63 Lund, Sweden.,Howard Hughes Medical Institute, University of California, Berkeley, CA, USA. doudna@berkeley.edu.,Experimental Therapeutics Centre, Agency for Science, Technology and Research (A(∗)STAR), 31 Biopolis way, Nanos, #03-01, Singapore 138669, Singapore. Electronic address: cbkang@etc.a-star.edu.sg.,Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan. yshiro@sci.u-hyogo.ac.jp sawai@sci.u-hyogo.ac.jp.,Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Via Ponte Don Melillo, 84084, Fisciano, SA, Italy.,Medicinal Chemistry, Department of Pharmacy and Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , U.K.,Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy.,Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA.,From the Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway.,the Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.,From the Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway, l.m.sollid@medisin.uio.no.,Worldwide Influenza Centre, Francis Crick Institute, NW1 1AT London, United Kingdom.,Department of Microbiology and Immunology, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA, 30322, USA.,National Research Center for Veterinary Medicine, Luoyang, Henan, China.,Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA. seok-yong.lee@duke.edu.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science, Mahidol University, Bangkok, 10400, Thailand; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand.,Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-106 91, Sweden.,Experimental Therapeutics Centre, Agency for Science, Technology and Research (A(∗)STAR), 31 Biopolis way, Nanos, #03-01, Singapore 138669, Singapore.,Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy.,Neuroscience Therapeutic Area, Neurodegeneration Research, Sanofi R&D, Chilly-Mazarin, France.,Manipal Academy of Higher Education, Karnataka, India.,International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.,Innovative Genomics Institute, University of California, Berkeley, CA, USA.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science, Mahidol University, Bangkok, 10400, Thailand. Electronic address: danaya.pak@mahidol.ac.th.,Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation.,Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), CEA, Université Paris-Saclay, Gif-sur-Yvette, France.,Institute for Research in Biomedicine, 6500 Bellinzona, Switzerland.,the Department of Gastroenterology, Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway, and.,Department of Systems Biology, Columbia University, New York, NY, USA. lss8@columbia.edu.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM), U1258/Centre National de la Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, 67404, Illkirch, France.,Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K. dmfvanaalten@dundee.ac.uk.,The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, 567-0047, Japan.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM), U1258/Centre National de la Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, 67404, Illkirch, France. Electronic address: rochel@igbmc.fr.,Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232.,Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA.,Department of Molecular Oncology, Genentech, South San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, CA, USA. enogales@lbl.gov.,Jenner Institute, University of Oxford, Oxford OX3 7FZ, UK.,European Molecular Biology Laboratory, Grenoble, France.,Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden. robert.gustafsson@dbb.su.se.,Humabs BioMed SA, 6500 Bellinzona, Switzerland.,the Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, Wales, United Kingdom.,Structural Biology of Cells and Viruses Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom; Donald.Benton@crick.ac.uk Peter.Rosenthal@crick.ac.uk John.Skehel@crick.ac.uk.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,Synthetic Biology and Bioengineering Research Center, KRIBB, Daejeon, 34141, Republic of Korea. sglee@kribb.re.kr.,MRC Laboratory of Molecular Biology, Cambridge, UK.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy; Pasteur Institute - Cenci Bolognetti Foundation, Sapienza Università di Roma, Viale Regina Elena 324, 00161, Rome, Italy. Electronic address: antonello.mai@uniroma1.it.,Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. enogales@lbl.gov.,Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, Université Paul Sabatier, 31077, Toulouse, France.,Institut du Thorax, Inserm UMR 1087/CNRS UMR 6291, LabEx "Ion Channels, Science and Therapeutics", Nantes, France.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.,Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom.,MRC Laboratory of Molecular Biology, Cambridge, UK. scheres@mrc-lmb.cam.ac.uk.,Structural Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom; Donald.Benton@crick.ac.uk Peter.Rosenthal@crick.ac.uk John.Skehel@crick.ac.uk.,the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute and.,Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. doudna@berkeley.edu.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia. anthony.purcell@monash.edu nathan.croft@monash.edu.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea. sglee@kribb.re.kr.,INSERM, UMR 1100, "Centre d'Etude des Pathologies Respiratoires", 37032 Tours, France; Université de Tours, 37032 Tours, France. Electronic address: brice.korkmaz@inserm.fr.,Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.,Institute of Biomedical Sciences , Academia Sinica , Taipei 11529 , Taiwan.,Smartox Biotechnology, Saint-Egrève, France.,Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India. Electronic address: nandhanu@gmail.com.,Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore.,Max-Planck-Institute for Biochemistry, Planegg, Germany.,Chemical & Physical Biology Program, Vanderbilt University, Nashville, TN 37235; james.crowe@vanderbilt.edu jens.meiler@vanderbilt.edu.,Department of Urology, Boston Children's Hospital, Department of Microbiology and Immunobiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA. sicai.zhang@childrens.harvard.edu.,Integrated Drug Discovery-High Content Biology, Sanofi R&D, Vitry-sur-Seine, France.,VTT Technical Research Center of Finland Ltd., Espoo, Finland.,Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Department of Urology, Boston Children's Hospital, Department of Microbiology and Immunobiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA.,Innovative Genomics Institute, University of California, Berkeley, CA, USA. doudna@berkeley.edu.,Department of Cellular and Molecular Pharmacology , University of California, San Francisco , San Francisco , California 94143 , United States.,Vanderbilt Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232.,Laboratory of Biomolecular Research, Paul Scherrer Institut, 5232, Villigen, Switzerland. kurt.ballmer-hofer@unibas.ch.,Ipsen Innovation, 5 Avenue du Canada, 91940 Les Ulis, France.,the K. G. Jebsen Centre for Coeliac Disease Research, University of Oslo, 0424 Oslo, Norway.,Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461.,Laboratory of Biomolecular Research, Paul Scherrer Institut, 5232, Villigen, Switzerland.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; baumeist@biochem.mpg.de.,Alchemical Dynamics s.r.l., 00125, Rome, Italy.,Department of Molecular Biology, Genentech, South San Francisco, CA, USA.,Department of Biomolecular Resources, Genentech, South San Francisco, CA, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN 37235.,Chemical & Physical Biology Program, Vanderbilt University, Nashville, TN 37235.,Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden. stenmark@dbb.su.se.,Chemistry and Chemical Biology Graduate Program , University of California, San Francisco , San Francisco , California 94143 , United States.,Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy. Electronic address: andrea.mattevi@unipv.it.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. lss8@columbia.edu.,Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu Province 210009, China.,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands.,Comprehensive Pneumology Center, Institute of Lung Biology and Disease, German Center for Lung Research (DZL), 81377 Munich, Germany; Max Planck Institute of Neurobiology, 82152 Planegg-Martinsried, Germany.,Institut des Neurosciences Paris-Saclay (Neuro-PSI), UMR CNRS/Université Paris-Sud 9197, Université Paris-Saclay, Gif-sur-Yvette, France.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. enogales@lbl.gov.,Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy and Harvard Medical School, Boston, MA, 02115, USA.,Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Chemistry, Boston University, Boston, MA, USA. drkallen@bu.edu.,Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461.,Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy; Gene Expression Laboratory, National Institute for Infectious Diseases "Lazzaro Spallanzani" I.R.C.C.S., Rome, Italy.,Department of Biology, Institute of Molecular Systems Biology,ETH Zurich, Zurich 8093, Switzerland.,Department of Electrical, Computer, and Energy Engineering , University of Colorado , Boulder , Colorado 80309 , United States.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM), U1258/Centre National de la Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, 67404, Illkirch, France. Electronic address: kieffer@igbmc.fr.,Integrated Drug Discovery-Synthetic Molecular Design, Sanofi R&D, Frankfurt, Germany.,Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-University, Munich, Germany.,Stratingh Institute for Chemistry, University of Groningen, 9747AG, Groningen, The Netherlands.,Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.,Institute of Infection and Immunity, Cardiff University School of Medicine,Heath Park, Cardiff CF14 4XN, UK.,Structural Biology Science Technology Platform, Francis Crick Institute, NW1 1AT London, United Kingdom.,Department of Pharmaceutical Chemistry , University of California, San Francisco , San Francisco , California 94143 , United States.,Department of Medicine, Division of Infectious Diseases, Albert Einstein College of Medicine, Bronx, NY 10461; johanna.daily@einstein.yu.edu vern.schramm@einstein.yu.edu.,National University of Singapore (Suzhou) Research Institute, Suzhou, Jiangsu, China.,Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore. Electronic address: luodahai@ntu.edu.sg.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. bh6@cumc.columbia.edu.,Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, MA, USA.,Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy and Harvard Medical School, Boston, MA, 02115, USA. I.vanRhijn@uu.nl.,Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy.,Department of Integrative Structural and Computational Biology, The Scripps Research Insititute, La Jolla, CA 92037, USA; Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK.,Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima 30000, Thailand.,Department of Systems Biology, Columbia University, New York, NY, USA. bh6@cumc.columbia.edu.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA.,the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute and Jamie.rossjohn@monash.edu.,Vaccine Research Center, NIH, Bethesda, MD 20892, USA.,Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.,Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. doudna@berkeley.edu.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. imper@mit.edu.,Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032, Marburg, Germany.,Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore.,Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland.,Synthetic Biology and Bioengineering Research Center, KRIBB, Daejeon, 34141, Republic of Korea.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand p.young@auckland.ac.nz n.moreland@auckland.ac.nz.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.,Department of Pathology, Genentech, South San Francisco, CA, USA.,INSERM, UMR 1100, "Centre d'Etude des Pathologies Respiratoires", 37032 Tours, France; Université de Tours, 37032 Tours, France.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,MedImmune LLC, Gaithersburg, MD 20878.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584CL, Utrecht, The Netherlands. I.vanRhijn@uu.nl.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia. Jamie.rossjohn@monash.edu.,Howard Hughes Medical Institute, Columbia University, New York, NY, USA. bh6@cumc.columbia.edu.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.,Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461; johanna.daily@einstein.yu.edu vern.schramm@einstein.yu.edu.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. sylviegtsodikova@uky.edu.,Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: jiang@scripps.edu.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. oleg.tsodikov@uky.edu.,Department of Medicine, Columbia University, New York, NY, USA. bh6@cumc.columbia.edu.,Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, Victoria 3800, Australia.,Department of Chemistry, University of California, Berkeley, CA, USA. doudna@berkeley.edu.,Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA. hannoush.rami@gene.com.,Department of Integrative Structural and Computational Biology, The Scripps Research Insititute, La Jolla, CA 92037, USA; Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; The Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA.,Department of Mathematics, MIT, Cambridge, MA, USA.,Clayton Foundation Laboratories of Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.,Zymeworks Inc, 540-1385 West 8th Avenue, Vancouver, BC, V6H 3V9, Canada.,Howard Hughes Medical Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.,Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada.,Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany. werner.kuehlbrandt@biophys.mpg.de t.meier@imperial.ac.uk.,Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany.,State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China.,Department of Structural Biology, Genentech, South San Francisco, CA, USA.,Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan.,Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461.,Department of Chemistry, Boston University, Boston, MA, USA.,Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea.,Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India. Electronic address: gunaunom@gmail.com.,State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China; Health Science Center, Peking University, Haidian District, Beijing 100191, China; School of Medicine, Nankai University, Nankai District, Tianjin 300071, China. Electronic address: yshao@bjmu.edu.cn.,School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , U.K.,Structural Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom.,Department of Chemistry, Vanderbilt University, Nashville, TN 37235.,The Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA 92037, USA.,Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.,Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany.,Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany.,Division of Biological Sciences, Poornaprajna Institute of Scientific Research, Bangalore, India.,Department of Urology, Boston Children's Hospital, Department of Microbiology and Immunobiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA. min.dong@childrens.harvard.edu.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037.,Department of Chemistry, University of Eastern Finland Joensuu Campus, Joensuu, Finland.,California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.,Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA. gouauxe@ohsu.edu.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia. Jamie.rossjohn@monash.edu.,Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA. imper@mit.edu.,Department of Systems Biology, Columbia University, New York, NY, USA.,Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, MA, USA. drkallen@bu.edu.,Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy; Gene Expression Laboratory, National Institute for Infectious Diseases "Lazzaro Spallanzani" I.R.C.C.S., Rome, Italy; Pasteur Institute - Cenci Bolognetti Foundation, Sapienza Università di Roma, Viale Regina Elena 324, 00161, Rome, Italy.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy. Electronic address: sergio.valente@uniroma1.it.,Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany.,Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics' of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation.,Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA. bh6@cumc.columbia.edu.,Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden. geoffrey.masuyer@dbb.su.se.,National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.,Department of Plant and Microbiology, University of California, Berkeley, CA, USA.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Therapeutic Discovery, Amgen Research , Amgen Inc. , 1120 Veterans Blvd , South San Francisco , California 94080 , United States.,Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA.,Department of Biophysics, Ruhr University Bochum, 44801 Bochum, Germany.,Institute of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK. Jamie.rossjohn@monash.edu.,Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.,Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India.,Department of Pathology and Laboratory Medicine, University of Kansas School of Medicine, Kansas City, KS, USA.,leadXpro AG, PARK INNOVAARE, 5234, Villigen, Switzerland.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea.,Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand p.young@auckland.ac.nz n.moreland@auckland.ac.nz.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232.,Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.,From the Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India and.,Centro Nazionale per il Controllo e la Valutazione dei Farmaci, Istituto Superiore di Sanità, Viale Regina Elena 299, I-00161, Rome, Italy.,Department of Mathematics, University of Leipzig, 04109 Leipzig, Germany.,California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA. enogales@lbl.gov.,Computational and Systems Biology, MIT, Cambridge, MA, USA.,Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany.,College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden.,MRC Laboratory of Molecular Biology, Cambridge, UK. mg@mrc-lmb.cam.ac.uk.,Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy. chiara.gabbiani@unipi.it.,Structural Biology of Cells and Viruses Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom.,Departments of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, 94720, USA.,Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA. lss8@columbia.edu.,Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,Neuprozyme Therapeutics A/S, 2970 Hörsholm, Denmark.,Gladstone Institutes, San Francisco, CA, USA. doudna@berkeley.edu.,Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy; Center for Life Nano Science@Sapienza, Italian Institute of Technology, Via Regina Elena 291, 00161, Rome, Italy.,From the Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India and bbiswal@nii.ac.in.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Science, School of Clinical Science, Monash University, Clayton, Victoria 3168, Australia.,Howard Hughes Medical Institute, Columbia University, New York, NY, USA.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584CL, Utrecht, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DQ alpha 1 chain
C, A
190Homo sapiensMutation(s): 0 
Gene Names: HLA-DQA1
Find proteins for P01909 (Homo sapiens)
Go to Gene View: HLA-DQA1
Go to UniProtKB:  P01909
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC class II HLA-DQ-beta-1 - DQ2-glia-alpha1 chimeric protein
E, F
226Homo sapiensMutation(s): 0 
Gene Names: HLA-DQB1
Find proteins for O19712 (Homo sapiens)
Go to Gene View: HLA-DQB1
Go to UniProtKB:  O19712
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.226α = 90.00
b = 101.968β = 91.78
c = 70.528γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2018-12-12
    Type: Data collection, Database references
  • Version 1.2: 2019-01-30
    Type: Data collection, Database references