5W46

Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Impact of different ionization states of phosphorylated Serine-65 on ubiquitin structure and interactions.

Kazansky, Y.Lai, M.Y.Singh, R.K.Fushman, D.

(2018) Sci Rep 8: 2651-2651

  • DOI: 10.1038/s41598-018-20860-w

  • PubMed Abstract: 
  • The covalent attachment of ubiquitin (Ub) or Ub chains to cellular proteins is a versatile post-translational modification involved in a variety of eukaryotic cellular events. Recently, the post-translational modification of Ub itself by phosphorylat ...

    The covalent attachment of ubiquitin (Ub) or Ub chains to cellular proteins is a versatile post-translational modification involved in a variety of eukaryotic cellular events. Recently, the post-translational modification of Ub itself by phosphorylation has emerged as an important component of the Ub-signaling system. Specifically, Ub phosphorylation at serine-65 was shown to activate parkin-mediated mitochondrial quality control. However, the impact of phosphorylation on Ub structure and interactions is poorly understood. Here we investigate the recently reported structural changes in Ub upon serine-65 phosphorylation, namely, the equilibrium between a native-like and a novel, alternate conformer of phosphorylated Ub (pUb). We show that this equilibrium is pH-dependent, and the two pUb conformers are linked to the different charge states of the phosphate group. We examined pUb binding to a known Ub-receptor and found that the alternate conformer is binding incompetent. Furthermore, serine-65 phosphorylation affects the conformational equilibrium of K48-linked Ub dimers. Lastly, our crystal structure of S65D Ub and NMR data indicate that phosphomimetic mutations do not adequately reproduce the salient features of pUb. Our results suggest that the pH-dependence of the conformations and binding properties of phosphorylated Ub and polyUb could provide an additional level of modulation in Ub-mediated signaling.


    Organizational Affiliation

    Department of Chemistry, Osaka Medical College, Takatsuki, 569-8686 Osaka, Japan; tokajima@sanken.osaka-u.ac.jp.,Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK; Structural Biology and Biophysics Unit, Fondazione Ri.MED, Via Bandiera, 11, 90133 Palermo, Italy.,Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143.,Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA.,Division of Structural Biology, University of Oxford, Headington, OX3 7BN Oxford, United Kingdom dave@strubi.ox.ac.uk qianp@mail.hzau.edu.cn louzy@mail.tsinghua.edu.cn.,Center of Biomedical Analysis, Tsinghua University, 100084, Beijing, China.,Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Germany.,Centre de Biologie Cellulaire de Montpellier, CNRS, University Montpellier, UMR5237, 34090 Montpellier, France.,Institute of Pharmaceutical Sciences, University of Freiburg, Germany.,Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland. Electronic address: lyam@chem.uw.edu.pl.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, 100083, Beijing, China. gzhao@cau.edu.cn.,Nanjing Foreign Language School, 210046 Nanjing, China.,Division of Structural Biology, University of Oxford, Headington, OX3 7BN Oxford, United Kingdom.,NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.,Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia.,Department of Pharmaceutical Sciences, College of Pharmacy , University of Kentucky , 789 South Limestone Street , Lexington , Kentucky 40536 , United States.,Global Biotherapeutics Technologies, Pfizer R&D, Grange Castle Business Park, Dublin D22, Ireland.,Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK. Electronic address: martin.noble@ncl.ac.uk.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA.,Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States.,Institute of Biochemistry and Biophysiscs, Polish Academy of Science, Laboratory of Biological NMR, Pawińskiego 5A, 02-106 Warszawa, Poland. Electronic address: aejchart@ibb.waw.pl.,Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China.,Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece.,School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , P.R. China.,School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney, NSW, 2052, Australia. h.rob.yang@unsw.edu.au.,Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, MA 01075, USA.,Department of Biochemistry and Biophysics , Oregon State University , Corvallis , Oregon 97331 , United States.,Amgen Research, Department of Cardiometabolic Disorders, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA.,School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney, NSW, 2052, Australia.,Instituto de Biociências, Letras e Ciências Exatas , Universidade Estadual Paulista , Rua Cristóvão Colombo , 2265 São José do Rio Preto , Brazil.,Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China. gaof@im.ac.cn.,Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK.,Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, 30302-3965.,School of Pharmaceutical Sciences; MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China.,Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan.,School of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Germany; Bioengineering and Biosystems, Institute of Functional Interfaces, Karlsruhe Institute of Technology, Germany.,Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands.,Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland. Electronic address: pawel.mak@uj.edu.pl.,From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea, wlee@spin.yonsei.ac.kr.,Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu, 215123, China.,Institute of Applied Biosciences, Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece.,Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK. alain.townsend@imm.ox.ac.uk.,Department of Biochemistry, Osaka Medical College, Takatsuki, 569-8686 Osaka, Japan.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.,Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Germany. Electronic address: franz-josef.meyer-almes@h-da.de.,Department of Chemistry, Osaka Medical College, Takatsuki, 569-8686 Osaka, Japan.,Department of Biomolecular Science and Reaction, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, 567-0047 Osaka, Japan.,Department of Biology, School of Arts & Sciences, University of Richmond , Richmond, Virginia 23173, United States.,Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Advanced Photon Source, Argonne, Illinois, USA.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, 100083, Beijing, China.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.,University of Wyoming School of Pharmacy, 1000 E. University Ave., HS 596, Laramie, WY, 82071, USA.,Division of Biomedical Sciences, School of Medicine , University of California Riverside , 900 University Avenue , Riverside , California 92521 , United States.,Department of Ophthalmology, University of California, San Francisco, CA 94158.,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Molecular Biosciences , The University of Texas at Austin , Austin , Texas 78712 , United States.,Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.,Department of Chemistry, Georgia State University, Atlanta, Georgia, 30302-3965.,Amgen Research, Department of Cardiometabolic Disorders, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA. dlloyd@amgen.com.,College of Life Sciences, Nankai University, 300071 Tianjin, China.,Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, La Rioja, Spain.,School of Medicine, Chang Gung University, Taoyuan, Taiwan. arthur1726@cgmh.org.tw.,Amgen Research, Department of Pharmacokinetics and Drug Metabolism, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA.,Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Molecular Biophysics Unit, Indian Institute of Science , Bangalore, Karnataka 560012, India.,California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720.,Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland; Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Kraków, Poland. Electronic address: grzegorz.dubin@uj.edu.pl.,National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, Republic of Korea. Electronic address: sangheelee@mju.ac.kr.,Chapman University School of Pharmacy (CUSP), Harry and Diane Rinker Health Science Campus, Chapman University, Irvine, CA, 92618, USA.,Protein Crystal Analysis Division, Structure Analysis Promotion Group, Japan Synchrotron Radiation Research Institute, Sayo-gun, 679-5198 Hyogo, Japan.,Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287.,Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; jfraser@fraserlab.com enogales@lbl.gov.,Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,School of Biological Sciences, Monash University, Melbourne, Australia.,Department of Engineering Physics, Tsinghua University, Beijing 100086, China.,Unité Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528, CNRS, 75015 Paris, France.,Neurimmune AG, Wagistrasse 13, 8952 Schlieren, Switzerland; Institute for Regenerative Medicine, University of Zurich, Wagistrasse 12, 8952 Schlieren, Switzerland.,From the Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand, greg.cook@otago.ac.nz.,Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu, 215123, China. jiaweiwu@suda.edu.cn.,Clinical and Research Center of Infectious Diseases, The National Clinical Key Department of Infectious Disease, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,From Global Biotherapeutics Technologies, Pfizer R&D, Cambridge, Massachusetts 02140 and joel.bard@pfizer.com.,Expression Génétique Microbienne , UMR 8261, CNRS, Université Paris, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie , 75005 Paris , France.,Advanced Photon Technology Division, RIKEN SPring-8 Center, Sayo-gun, 679-5148 Hyogo, Japan.,From Global Biotherapeutics Technologies, Pfizer R&D, Cambridge, Massachusetts 02140 and.,State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062, China.,Department of Biochemistry, College of Natural and Agricultural Sciences , University of California Riverside , 900 University Avenue , Riverside , California 92521 , United States.,Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA. fushman@umd.edu.,Amgen Research, Comparative Biology and Safety Sciences, Amgen Inc., 360 Binney St., Cambridge, MA 02141, USA.,Department of Chemistry, Stanford University, Stanford, CA, 94305-5080, USA.,From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea.,From the Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.,Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia, 30302-3965.,Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States.,College of Veterinary Medicine, China Agricultural University, Beijing, China.,Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,NMR Research Center, Indian Institute of Science , Bangalore, Karnataka 560012, India.,Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK. Electronic address: mathew.martin@ncl.ac.uk.,Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland. Electronic address: benedykt.wladyka@uj.edu.pl.,Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Brisbane, Queensland 4111, Australia.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China. Electronic address: chenzhongzhou@cau.edu.cn.,Research School of Chemistry, The Australian National University, Canberra, Australia.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China. shiyi@im.ac.cn.,Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.,Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Center for translational Immunology, Chinese Academy of Medical Science Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, UK.,Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece.,National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, 100101 Beijing, China.,Institute of Pharmaceutical Chemistry, University Frankfurt, Germany.,School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, 116034, Dalian, China. duming@dlpu.edu.cn.,School of Life and Environmental Sciences, Deakin University, Melbourne, Victoria, Australia.,Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.,School of Life Sciences, University of Science and Technology of China, Anhui, 230026, China.,Department of Microbiology and Immunology, University of Michigan Medical School, 5641 Medical Science Building II, 1150 West Medical Center Drive, Ann Arbor, MI 48109-0620, USA.,Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, 100084 Beijing, China; dave@strubi.ox.ac.uk qianp@mail.hzau.edu.cn louzy@mail.tsinghua.edu.cn.,Amgen Research, Department of Therapeutic Discovery, Amgen Inc., 7990 Enterprise Street, Burnaby, BC V5A 1V7, Canada.,Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, China.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA. vddonk@illinois.edu.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.,Tsinghua University Affiliated High School, 100084 Beijing, China.,Howard Hughes Medical Institute, Oregon Health & Science University, Portland, Oregon, United States of America.,Amgen Research, Department of Cardiometabolic Disorders, Amgen Inc., 1120 Veterans Blvd., South San Francisco, CA 94080, USA.,Biogen, 225 Binney Street, Cambridge, MA 02142, USA. Electronic address: paul.weinreb@biogen.com.,Department of Cardiovascular Surgery, Min-Sheng General Hospital, Taoyuan, Taiwan.,Department of Biochemistry , Duke University , Durham , North Carolina 27710 , United States.,Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia. Electronic address: jaremko@gmail.com.,Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025-7015, USA.,Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Brisbane, Queensland 4111, Australia. Electronic address: s.poulsen@griffith.edu.au.,School of Life Sciences, Tsinghua University, 100084 Beijing, China.,The Commonwealth Scientific and Industrial Research Organisation, Land and Water Flagship, Canberra, Australian Capital Territory, Australia, and chris.greening@monash.edu.,Division of Hematology, The Children's Hospital of Philadelphia , Philadelphia, Pennsylvania 19104, United States.,Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory for Protein Science, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China. jiaweiwu@suda.edu.cn.,Howard Hughes Medical Institute, University of California, Berkeley, CA 94720.,The Ohio State University College of Medicine, 473 W 12th Ave, Columbus, OH, 43210, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94143.,Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, 100084 Beijing, China.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand.,Division of Infectious Diseases, Department of Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Sorbonne Universités, Université Pierre et Marie Curie, 75006 Paris, France.,Bioengineering and Biosystems, Institute of Functional Interfaces, Karlsruhe Institute of Technology, Germany.,Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China, hgliu@csrc.ac.cn.,Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory for Protein Science, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.,The Commonwealth Scientific and Industrial Research Organisation, Land and Water Flagship, Canberra, Australian Capital Territory, Australia, and.,Amgen Research, Department of Therapeutic Discovery, Amgen Inc., 1120 Veterans Blvd., South San Francisco, CA 94080, USA.,Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Center for Influenza Research and Early-Warning, Chinese Academy of Sciences, Beijing, China. gaof@im.ac.cn.,Global Biotherapeutics Technologies, Pfizer R&D, Grange Castle Business Park, Dublin D22, Ireland orla.cunningham@pfizer.com.,Vollum Institute, Oregon Health & Science University, Portland, Oregon, United States of America.,Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.,Department of Microbiology, Immunology and Tropical Medicine and Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University , Washington D.C. 20037, United States.,Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States.,Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas , Universidade Federal de Minas Gerais , Av. Antônio Carlos , 6627 Belo Horizonte , Brazil.,School of Biology, Centers for Georgia State University, Atlanta, Georgia, 30302-3965.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA. s-nair@life.uiuc.edu.,Center for Influenza Research and Early-Warning, Chinese Academy of Sciences, Beijing, China. shiyi@im.ac.cn.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA. s-nair@life.uiuc.edu.,Research School of Chemistry, The Australian National University, Canberra, Australia, colin.jackson@anu.edu.au.,CSIRO, 343 Royal Parade, Parkville, Melbourne, Victoria 3052, Australia.,Department of Chemistry and Biochemistry , Utah State University , Logan , Utah 84322 , United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; jfraser@fraserlab.com enogales@lbl.gov.,Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143; david.julius@ucsf.edu yifan.cheng@ucsf.edu jenny.vanderwijst@radboudumc.nl.,Unité Récepteurs-canaux, Institut Pasteur, UMR 3571, CNRS, 75015 Paris, France.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Champaign, IL, USA. vddonk@illinois.edu.,Department of Physiology, University of California, San Francisco, CA 94143 david.julius@ucsf.edu yifan.cheng@ucsf.edu jenny.vanderwijst@radboudumc.nl.,Unité Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528, CNRS, 75015 Paris, France; marc.delarue@pasteur.fr.,National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, Republic of Korea.,The Pirbright Institute, Pirbright, Woking, UK.,Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University , Cairns 4870, Queensland Australia.,Amgen Research, Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA.,Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China. shiyi@im.ac.cn.,Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA. mochly@stanford.edu.,Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, PO Box 596, SE-751 24 Uppsala, Sweden.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158.,Departamento de Microbiología, Facultad de Salud , Universidad del Valle , Calle 4B No. 36-00 Cali , Colombia.,Center for translational Immunology, Chinese Academy of Medical Science Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, UK. alain.townsend@imm.ox.ac.uk.,Biogen, 225 Binney Street, Cambridge, MA 02142, USA.,Department of Chemistry and Biochemistry, Knoebel Institute for Healthy Aging , University of Denver , Denver , Colorado 80208 , United States.,Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK. Electronic address: rivka.isaacson@kcl.ac.uk.,Hubei Colorectal Cancer Clinical Research Center, Hubei Cancer Hospital, 430071 Wuhan, China.,Pediatric Dentistry and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA. vddonk@illinois.edu.,Drug Discovery Center for Infectious Disease, College of Pharmacy, Nankai University, 300071 Tianjin, China.,Biogen, 225 Binney Street, Cambridge, MA 02142, USA; Neurimmune AG, Wagistrasse 13, 8952 Schlieren, Switzerland. Electronic address: andreas.weihofen@biogen.com.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China.,Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK.,Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China. gaof@im.ac.cn.,Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France , Université Pierre et Marie Curie , 11 place Marcelin Berthelot , 75231 Paris Cedex 05 , France.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China; dave@strubi.ox.ac.uk qianp@mail.hzau.edu.cn louzy@mail.tsinghua.edu.cn.,Departamento de Microbiologia, Instituto de Ciências Biomédicas , Universidade de São Paulo , Avenida Prof. Lineu Prestes , 1374 São Paulo , Brazil.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.,Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul 03722, South Korea.,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA champy@uab.edu.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and.,Laboratoire de Biochimie Théorique, CNRS UPR9080 , Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie , 75005 Paris , France.,Neurimmune AG, Wagistrasse 13, 8952 Schlieren, Switzerland.,Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan. arthur1726@cgmh.org.tw.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
A, B
76Homo sapiensMutation(s): 1 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 33.456α = 90.00
b = 48.248β = 99.03
c = 41.707γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
Cootmodel building
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM065334

Revision History 

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence
  • Version 1.2: 2019-01-16
    Type: Data collection, Database references