5XMF

Crystal structure of feline MHC class I for 2,1 angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Major Histocompatibility Complex Class I (FLA-E*01801) Molecular Structure in Domestic Cats Demonstrates Species-Specific Characteristics in Presenting Viral Antigen Peptides

Liang, R.Sun, Y.Liu, Y.Wang, J.Wu, Y.Li, Z.Ma, L.Zhang, N.Zhang, L.Wei, X.Qu, Z.Zhang, N.Xia, C.

(2018) J. Virol. 92: --

  • DOI: 10.1128/JVI.01631-17
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Feline immunodeficiency virus (FIV) infection in domestic cats is the smallest usable natural model for lentiviral infection studies. FLA-E*01801 was applied to FIV AIDS vaccine research. We determined the crystal structure of FLA-E*01801 complexed w ...

    Feline immunodeficiency virus (FIV) infection in domestic cats is the smallest usable natural model for lentiviral infection studies. FLA-E*01801 was applied to FIV AIDS vaccine research. We determined the crystal structure of FLA-E*01801 complexed with a peptide derived from FIV (gag positions 40 to 48; RMANVSTGR [RMA9]). The A pocket of the FLA-E*01801 complex plays a valuable restrictive role in peptide binding. Mutation experiments and circular-dichroism (CD) spectroscopy revealed that peptides with Asp at the first position (P1) could not bind to FLA-E*01801. The crystal structure and in vitro refolding of the mutant FLA-E*01801 complex demonstrated that Glu 63 and Trp 167 in the A pocket play important roles in restricting P1D. The B pocket of the FLA-E*01801 complex accommodates M/T/A/V/I/L/S residues, whereas the negatively charged F pocket prefers R/K residues. Based on the peptide binding motif, 125 FLA-E*01801-restricted FIV nonapeptides (San Diego isolate) were identified. Our results provide the structural basis for peptide presentation by the FLA-E*01801 molecule, especially A pocket restriction on peptide binding, and identify the potential cytotoxic T lymphocyte (CTL) epitope peptides of FIV presented by FLA-E*01801. These results will benefit both the reasonable design of FLA-E*01801-restricted CTL epitopes and the further development of the AIDS vaccine. IMPORTANCE Feline immunodeficiency virus (FIV) is a viral pathogen in cats, and this infection is the smallest usable natural model for lentivirus infection studies. To examine how FLA I presents FIV epitope peptides, we crystallized and solved the first classic feline major histocompatibility complex class I (MHC-I) molecular structure. Surprisingly, pocket A restricts peptide binding. Trp 167 blocks the left side of pocket A, causing P1D to conflict with Glu 63 We also identified the FLA-E*01801 binding motif X (except D)-(M/T/A/V/I/L/S)-X-X-X-X-X-X-(R/K) based on structural and biochemical experiments. We identified 125 FLA-E*01801-restricted nonapeptides from FIV. These results are valuable for developing peptide-based FIV and human immunodeficiency virus (HIV) vaccines and for studying how MHC-I molecules present peptides.


    Organizational Affiliation

    Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Braunschweig, Germany.,Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.,Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, Haidian District, Beijing, China.,Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil. Electronic address: carlos.bloch@embrapa.br.,Gorlaeus Laboratories , Leiden Institute of Chemistry and Netherlands Proteomics Centre , Einsteinweg 55 , 2333 CC Leiden , Netherlands.,Department of Molecular and Systems Biology and Norris Cotton Cancer Center , Geisel School of Medicine at Dartmouth , 1 Medical Centre Drive HB7936 , Lebanon , New Hampshire 03756 , United States.,Center of Pharmaceutical Engeneering (PVZ), Technische Universität Braunschweig, Braunschweig, Germany.,Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.,Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, China.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.,Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea. Electronic address: eunice@kist.re.kr.,College of Life Sciences, Peking University, Beijing 100871, China.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3C 3J7, Canada.,School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.,RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China.,Department of Biochemistry and the Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Institute of Biochemistry, University of Cologne, 50674 Koeln, Germany.,Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea.,ManRos Therapeutics, Hôtel de Recherche, Centre de Perharidy, Roscoff, France.,Olema Pharmaceuticals, San Francisco, CA, 94107, USA. leslie@olemapharma.com.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. kurumizaka@iam.u-tokyo.ac.jp shunichi.sekine@riken.jp.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6059, USA. blackbe@pennmedicine.upenn.edu.,Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie , Technische Universität München , 85748 Garching , Germany.,Tetramer Core, BRI at Virginia Mason, Seattle, WA, USA.,Translational Research Program, BRI at Virginia Mason, Seattle, WA, USA.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Chemistry , University of Florence , Via della Lastruccia 3 , 50019 Sesto Fiorentino, Florence , Italy.,Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China. kuangty@ibcas.ac.cn.,Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, F-38043, Grenoble, France. christoph.mueller_dieckmann@esrf.fr.,Departamento de Química, Universidade Federal de São Carlos (UFSCar), São Carlos, São Paulo, Brazil.,Instituto de Química, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil; Instituto de Biociências, Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil.,Division of Structural Biology, Department of Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Yahaba, Japan.,Ben May Department for Cancer Research, University of Chicago, Chicago, IL, 60637, USA. sfanning@uchicago.edu.,Olema Pharmaceuticals, San Francisco, CA, 94107, USA.,Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture, Institute of Apiculture, Chinese Academy of Agricultural Sciences, Beijing, China.,Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Republic of Korea ygkim76@postech.ac.kr.,Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, F-38043, Grenoble, France.,Department of Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel.,Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk, 37673, Republic of Korea.,Takeda California, Inc. , 10410 Science Center Drive , San Diego , California 92121 , United States.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA. vprasad@bcm.edu.,Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea.,Université de Lorraine, INRA, IAM, Nancy, France. eric.gelhaye@univ-lorraine.fr.,Department of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.,Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.,Ben May Department for Cancer Research, University of Chicago, Chicago, IL, 60637, USA.,Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA. qinj@ccf.org.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3C 3J7, Canada. john.pascal@umontreal.ca.,High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Center, Mumbai 400 085, India.,Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA. qinj@ccf.org.,Graduate School of Innovative Life Science , University of Toyama , 2630 Sugitani , Toyama 930-0194 , Japan.,Institute for Interdisciplinary Science, Okayama University, Okayama, Japan.,Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China. Electronic address: yunch@hsc.pku.edu.cn.,Department of Neuroscience, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea. Electronic address: ehur1@snu.ac.kr.,Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. kurumizaka@iam.u-tokyo.ac.jp shunichi.sekine@riken.jp.,Department of Chemistry, Université de Montréal, Montréal, QC, H3C 3J7, Canada.,Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada.,Computational Biochemistry, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6059, USA.,Université de Lorraine, CNRS, CRM2, Nancy, France. claude.didierjean@univ-lorraine.fr.,Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,DISFARM, Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica, Università degli Studi, Milano, Italy.,Université de Lorraine, INRA, IAM, Nancy, France.,Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan.,Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China. suisf@mail.tsinghua.edu.cn.,Max-Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.,Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA.,Institute for Pharmaceutical Chemistry, Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Pfizer Worldwide Research & Development , 610 Main Street, Cambridge, Massachusetts 02139, United States.,Abteilung Physikalische Biochemie, Max-Planck-Institut für molekulare Physiologie, Dortmund, Germany.,Instituto de Química, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil; Departamento de Áreas Acadêmicas, Instituto Federal de Educação, Ciência e Tecnologia e Goiás (IFG), Luziânia, Goiás, Brazil.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden. Electronic address: Vivianne.malmstrom@ki.se.,Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China zhangnianzhi@cau.edu.cn xiachun@cau.edu.cn.,Chemical Biology, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.,Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.,Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea.,Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany.,Brain Science Institute, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Department of Neuroscience, Korea University of Science and Technology, Daejeon, Republic of Korea; Department of Neuroscience, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea.,Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Republic of Korea.,Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands.,Neuroscience Drug Discovery Unit, Research , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome, Fujisawa , Kanagawa 251-8555 , Japan.,Université de Lorraine, LERMAB, Nancy, France.,Magnetic Resonance Center CERM , University of Florence , Via Luigi Sacconi 6 , 50019 Sesto Fiorentino, Florence , Italy.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. vprasad@bcm.edu.,Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453 552, India.,Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom.,The Francis Crick Institute, London, NW1 1AT, United Kingdom.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,Department of Hematology and Oncology , Kantonsspital St. Gallen , 9007 St. Gallen , Switzerland.,Department of Biochemical Sciences A.Rossi-Fanelli, University of Rome La Sapienza, Rome, Italy.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medical Sciences, Rheumatology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Université de Lorraine, CNRS, CRM2, Nancy, France.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Faculty of Pharmaceutical Sciences , University of Toyama , 2630 Sugitani , Toyama 930-0914 , Japan.,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.,Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil.,School of Biological Science and Technology, University of Jinan, Jinan, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MHC class I antigen alpha chain
A
275Felis catusMutation(s): 0 
Gene Names: FLA-I (FLAI-K)
Find proteins for C6ZK72 (Felis catus)
Go to UniProtKB:  C6ZK72
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
99Felis catusMutation(s): 0 
Gene Names: B2M
Find proteins for Q5MGS7 (Felis catus)
Go to Gene View: B2M
Go to UniProtKB:  Q5MGS7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Gag polyprotein
C
9Feline immunodeficiency virus (isolate Petaluma)Mutation(s): 0 
Gene Names: gag
Find proteins for P16087 (Feline immunodeficiency virus (isolate Petaluma))
Go to UniProtKB:  P16087
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.421α = 90.00
b = 83.379β = 90.00
c = 121.636γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the 973 Project of the China Ministry of Science and TechnologyChinaNO.2013CB835302
state key program of the National Natural Science Foundation of ChinaChinaNO. 31201887
the 863 Project of the China Ministry of Science and TechnologyChinaNO. 2013AA102503

Revision History 

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2019-01-16
    Type: Data collection, Database references