5CS7

The crystal structure of wt beta2-microglobulin at room temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Conformational dynamics in crystals reveal the molecular bases for D76N beta-2 microglobulin aggregation propensity.

Le Marchand, T.de Rosa, M.Salvi, N.Sala, B.M.Andreas, L.B.Barbet-Massin, E.Sormanni, P.Barbiroli, A.Porcari, R.Sousa Mota, C.de Sanctis, D.Bolognesi, M.Emsley, L.Bellotti, V.Blackledge, M.Camilloni, C.Pintacuda, G.Ricagno, S.

(2018) Nat Commun 9: 1658-1658

  • DOI: 10.1038/s41467-018-04078-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Spontaneous aggregation of folded and soluble native proteins in vivo is still a poorly understood process. A prototypic example is the D76N mutant of beta-2 microglobulin (β2m) that displays an aggressive aggregation propensity. Here we investigate ...

    Spontaneous aggregation of folded and soluble native proteins in vivo is still a poorly understood process. A prototypic example is the D76N mutant of beta-2 microglobulin (β2m) that displays an aggressive aggregation propensity. Here we investigate the dynamics of β2m by X-ray crystallography, solid-state NMR, and molecular dynamics simulations to unveil the effects of the D76N mutation. Taken together, our data highlight the presence of minor disordered substates in crystalline β2m. The destabilization of the outer strands of D76N β2m accounts for the increased aggregation propensity. Furthermore, the computational modeling reveals a network of interactions with residue D76 as a keystone: this model allows predicting the stability of several point mutants. Overall, our study shows how the study of intrinsic dynamics in crystallo can provide crucial answers on protein stability and aggregation propensity. The comprehensive approach here presented may well be suited for the study of other folded amyloidogenic proteins.


    Organizational Affiliation

    California Institute for Quantitative Biosciences, University of California, Berkeley, United States.,Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany. gratz.andreas@gmail.com.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: nathanael_gray@dfci.harvard.edu.,College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China. Electronic address: weifei_c@nwsuaf.edu.cn.,National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, and Center for Food Safety and Toxicology, Seoul National University, Seoul, South Korea.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. laub@mit.edu.,Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France. andre.zapun@ibs.fr.,Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, China.,Mitchell Cancer Institute, The University of South Alabama, Mobile, Alabama.,Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,From the Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA.,Howard Hughes Medical Institute, University of California, Berkeley, United States.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. yiorgo@stanford.edu.,Department of Biotechnology , The University of Tokyo , 1-1-1 Yayoi , Bunkyo-ku, Tokyo 113-8657 , Japan.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China; LBPA, ENS de Cachan, Université Paris-Saclay, Centre National de la Recherche Scientifique, 61 Avenue du Président Wilson, 94235, Cachan, France. Electronic address: xxi01@ens-cachan.fr.,Centre for Bacterial Cell Biology, Institute for Cell and Molecular Bioscience, Newcastle University, Newcastle Upon Tyne, NE2 4AX, United Kingdom.,David Geffen School of Medicine, University of California Los Angeles and Greater West Los Angeles Health Care System, Los Angeles, CA 90095, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA. kyle.l.brown@vanderbilt.edu.,College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.,the Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, Florida 32224.,Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. jmm@sund.ku.dk.,Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo 060-8589, Japan.,Heptares Therapeutics Ltd. , BioPark , Welwyn Garden City , Hertfordshire AL7 3AX , U.K.,Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy. stefano.ricagno@unimi.it.,Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,From the Departments of Biological Chemistry and Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA-DOE Institute, UCLA, Los Angeles, California 90095 and.,Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea mhk8n@kribb.re.kr choish@snu.ac.kr.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Chemical and Physical Biology, Vanderbilt University, Nashville, Tennessee.,Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy.,York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.,Department of Chemistry, Sejong University, Seoul, South Korea.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Porto, Portugal.,Department of Clinical Science, Kumamoto University Hospital, Kumamoto, 860-8556, Japan.,Department of Molecular and Cell Biology, University of California, Berkeley, United States.,High Magnet Field Laboratory, Chinese Academy of Science, 50 Shushanhu Road, Hefei, Anhui 230031, China.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: peter_sorger@hms.harvard.edu.,Aspirnaut Summer research program, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. yiorgo@stanford.edu.,Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.,Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany. wuensch@uni-muenster.de.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.,National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, and Center for Food Safety and Toxicology, Seoul National University, Seoul, South Korea mhk8n@kribb.re.kr choish@snu.ac.kr.,Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.,Institut für Biochemie, Department für Chemie, Universität zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany. Alexander.Schnitzler@posteo.de.,Veterans Affairs Hospital, Nashville, TN, 37232, USA.,School of Biological Sciences , Nanyang Technological University , 50 Nanyang Drive , Singapore 637551.,DuPont Nutrition and Health, 3329 Agriculture Dr, Madison, WI, 53716, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy. carlo.camilloni@unimi.it.,Leadership Alliance, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, United Kingdom.,Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, University College London, London, NW3 2PF, UK.,Northeastern Collaborative Access Team, Argonne National Laboratory, Lemont, IL, 60439, USA.,Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada; Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Bioinformatics Institute , ASTAR (Agency for Science, Technology and Research) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 . Email: chandra@bii.a-star.edu.sg ; Tel: +65 6478 8273.,Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec City, QC, G1V 4G2, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada. sylvain.moineau@bcm.ulaval.ca.,Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.,the Molecular Biophysics and Integrated Bioimaging Division, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and.,Koch Institute for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States.,From the Departments of Biological Chemistry and Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA-DOE Institute, UCLA, Los Angeles, California 90095 and david@mbi.ucla.edu.,ConfometRx, Santa Clara, CA, USA. kobilka@stanford.edu.,CryoEM Shared Resources, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA.,Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.,James Cook University, Cairns, Australia.,Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, 3584, The Netherlands.,Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France. guido.pintacuda@ens-lyon.fr.,The University of New South Wales, Faculty of Medicine, St Vincent's Clinical School, Darlinghurst, Sydney, NSW, 2010, Australia.,California NanoSystems Institute, University California Los Angeles, Los Angeles, CA 90095, USA.,Department of Chemistry, University of Duisburg-Essen, Essen, Germany.,HudsonAlpha Institute for Biotechnology, Huntsville, Alabama.,Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, BC, Canada.,Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA. laub@mit.edu.,Division of Molecular Biotherapy, Cancer Chemotherapy Center , Japanese Foundation for Cancer Research , 3-8-31 Ariake , Koto-ku, Tokyo 135-8850 , Japan.,Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France.,Departamento de Química, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, BC, Canada. ncjs@mail.ubc.ca.,Merck & Co., Department of Biochemical Engineering and Structure, 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA.,The Pirbright Institute, Pirbright, Woking, United Kingdom.,The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.,Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543.,Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques UMR 8601 CNRS, Sorbonne Paris Cité (USPC), Paris, 75006, France.,Life Sciences Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.,Dahlem Centre of Plant Sciences, Department of Plant Physiology and Biochemistry, Freie Universität Berlin, Königin-Luise-Straße 12-16, 14195, Berlin, Germany.,Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China. Electronic address: qma@qdio.ac.cn.,Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.,DuPont Nutrition and Health, BP 10, 86220, Dangé-Saint-Romain, France.,p53 Laboratory , ASTAR (Agency for Science, Technology and Research) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648 . Email: cjbrown@p53lab.a-star.edu.sg ; Tel: +65 6478 8273.,ESRF - The European Synchrotron, 38043, Grenoble, France.,Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432, Norway.,Department of Physiology, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin.,Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, 860-0082, Japan.,Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan. y-yasutake@aist.go.jp.,ConfometRx, Santa Clara, CA, USA.,Center for Environmental Health Sciences MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.,Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, 20133, Milano, Italy.,National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA. kyle.l.brown@vanderbilt.edu.,the Department of Medicine, University of California San Diego, La Jolla, California 92037, and.,Department of Cell Biology, Neurobiology and Anatomy and.,Medizinische Biochemie und Molekularbiologie, Universität des Saarlandes, Kirrberger Str., Geb. 44, D-66421 Homburg, Germany. michaelweyrich@gmx.de.,Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133, Milano, Italy.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan. kmaeda@ri.ncgm.go.jp.,Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo 060-8589, Japan. Electronic address: hmori@chem.agr.hokudai.ac.jp.,Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal.,Ipsen Bioscience , 650 East Kendall Street , Cambridge , MA 02142 , USA.,Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,School of Veterinary Sciences, University of Bristol, Bristol, United Kingdom.,Department of Agrifood Production and Environmental Sciences, University of Florence, Florence, Italy.,Institut für Biochemie, Department für Chemie, Universität zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany. kucklaen@uni-duesseldorf.de.,Immunology Division, Garvan Institute of Medical Research, 384 Victoria Road, Darlinghurst, Sydney, NSW, 2010, Australia. d.langley@garvan.org.au.,Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; German Center for Infection Research (DZIF), Hamburg - Lübeck - Borstel - Riems Site, University of Lübeck, Germany. Electronic address: hilgenfeld@biochem.uni-luebeck.de.,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,Division of Plant Biology, Department of Biosciences, University of Helsinki, FIN-00014, Helsinki, Finland.,NDBio Therapeutics Inc., Incheon 21984, Republic of Korea.,Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232-2372, USA.,the Stanford Synchrotron Radiation Light Source, Menlo Park, California 94025.,Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Center for Structural Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany.,Ipsen Innovation , 5, Avenue du Canada , Les Ulis , France 91940 . Email: sergeauvin@gmail.com ; Tel: +33 160 922481.,Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.,Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Life Sciences (BMLS) and Structural Genomics Consortium Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; German Cancer Network (DKTK), Frankfurt Site, 60438 Frankfurt am Main, Germany.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.,Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. kobilka@stanford.edu.,Institut de Biologie Structurale, CNRS, CEA, UGA, 30044, Grenoble, France.,the Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224, radisky.evette@mayo.edu.,From the Division of Immune Regulation, La Jolla Institute for Allergy and Immunology (LJI), La Jolla, California 92037.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada. sylvain.moineau@bcm.ulaval.ca.,Univ. Lyon, ENS de Lyon, Univ. Claude Bernard, CNRS UMR 5239, INSERM U1210, LBMC, 46 allée d'Italie Site Jacques Monod, F-69007, Lyon, France.,Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany. joachim.jose@uni-muenster.de.,RIKEN Program for Drug Discovery and Medical Technology Platforms , 2-1 Hirosawa , Wako , Saitama 351-0198 , Japan.,HudsonAlpha Institute for Biotechnology, Huntsville, Alabama; jprokop54@gmail.com jlazar@hudsonalpha.org.,From the Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel, papo@bgu.ac.il.,the Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224.,National Magnetic Resonance Facility at Madison , University of Wisconsin-Madison , 433 Babcock Drive , Madison , Wisconsin 53706 , United States.,Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.,Gene Expression & Regulation Program, Wistar Institute, Philadelphia, Pennsylvania.,Medizinische Biochemie und Molekularbiologie, Universität des Saarlandes, Kirrberger Str., Geb. 44, D-66421 Homburg, Germany. claudia.goetz@uks.eu.,Center for Structural Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA. kyle.l.brown@vanderbilt.edu.,the Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel.,HRMEM Facility, University of British Columbia, Vancouver, BC, Canada.,the National Institute for Biotechnology in the Negev (NIBN), Beer-Sheva 84105, Israel.,Systems Immunity Research Institute, Cardiff University, Cardiff, Wales, United Kingdom.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA. Electronic address: nkoropat@umich.edu.,the Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium.,CryoEM Shared Resources, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA. yuz@janelia.hhmi.org.,Farncombe Family Digestive Health Research Institute, McMaster University. Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada.,Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Life Sciences (BMLS) and Structural Genomics Consortium Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France.,Section on Nephrology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina; and.,Immunology Division, Garvan Institute of Medical Research, 384 Victoria Road, Darlinghurst, Sydney, NSW, 2010, Australia.,Medicinal Chemistry Research Group, Research Centre for Natural Sciences , Hungarian Academy of Sciences , 2 Magyar tudósok körútja , Budapest H-1117 , Hungary.,Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany. karsten.niefind@uni-koeln.de.,Faculty of Advanced Life Science, Hokkaido University, N-10, W-8, Sapporo 060-0810, Japan.,Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama.,Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada.,Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany. andre.bo@web.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
A
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.174 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 59.630α = 90.00
b = 29.240β = 102.89
c = 65.956γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2018-06-27
    Type: Data collection, Database references