5YMW

Crystal structure of 8-mer peptide from Rous sarcoma virus in complex with BF2*1201


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.997 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An Invariant Arginine in Common with MHC Class II Allows Extension at the C-Terminal End of Peptides Bound to Chicken MHC Class I.

Xiao, J.Xiang, W.Zhang, Y.Peng, W.Zhao, M.Niu, L.Chai, Y.Qi, J.Wang, F.Qi, P.Pan, C.Han, L.Wang, M.Kaufman, J.Gao, G.F.Liu, W.J.

(2018) J Immunol. 201: 3084-3095

  • DOI: 10.4049/jimmunol.1800611
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • MHC molecules are found in all jawed vertebrates and are known to present peptides to T lymphocytes. In mammals, peptides can hang out either end of the peptide-binding groove of classical class II molecules, whereas the N and C termini of peptides a ...

    MHC molecules are found in all jawed vertebrates and are known to present peptides to T lymphocytes. In mammals, peptides can hang out either end of the peptide-binding groove of classical class II molecules, whereas the N and C termini of peptides are typically tightly bound to specific pockets in classical class I molecules. The chicken MHC, like many nonmammalian vertebrates, has a single dominantly expressed classical class I molecule encoded by the BF2 locus. We determined the structures of BF2*1201 bound to two peptides and found that the C terminus of one peptide hangs outside of the groove with a conformation much like the peptides bound to class II molecules. We found that BF2*1201 binds many peptides that hang out of the groove at the C terminus, and the sequences and structures of this MHC class I allele were determined to investigate the basis for this phenomenon. The classical class I molecules of mammals have a nearly invariant Tyr (Tyr 84 in humans) that coordinates the peptide C terminus, but all classical class I molecules outside of mammals have an Arg in that position in common with mammalian class II molecules. We find that this invariant Arg residue switches conformation to allow peptides to hang out of the groove of BF2*1201, suggesting that this phenomenon is common in chickens and other nonmammalian vertebrates, perhaps allowing the single dominantly expressed class I molecule to bind a larger repertoire of peptides.


    Organizational Affiliation

    College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.,Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; liujun@ivdc.chinacdc.cn gaof@im.ac.cn jfk31@cam.ac.uk.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China; liujun@ivdc.chinacdc.cn gaof@im.ac.cn jfk31@cam.ac.uk.,NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,China Research Network of Immunity and Health, Beijing Institutes of Life Science Chinese Academy of Sciences, Beijing 100101, China.,Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Engineering and Technology Research Center for Beijing Veterinary Peptide Vaccine Design and Preparation, Zhongmu Institutes of China Animal Husbandry Industry Co. Ltd., Beijing 100095, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Department of Veterinary Medicine, University of Cambridge, Cambridge CB2 1QP, United Kingdom; and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Class I histocompatibility antigen, F10 alpha chain
A, D, G, J
271Gallus gallusMutation(s): 0 
Find proteins for P15979 (Gallus gallus)
Go to UniProtKB:  P15979
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, E, H, K
98Gallus gallusMutation(s): 0 
Gene Names: B2M
Find proteins for P21611 (Gallus gallus)
Go to Gene View: B2M
Go to UniProtKB:  P21611
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL
C, F, I, L
8Rous sarcoma virus (strain Prague C)Mutation(s): 0 
Gene Names: V-SRC
EC: 2.7.10.2
Find proteins for P00526 (Rous sarcoma virus (strain Prague C))
Go to UniProtKB:  P00526
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.997 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 86.817α = 90.00
b = 117.268β = 111.21
c = 92.507γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
SCALEPACKdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2019-07-31
    Type: Data collection, Database references