6IEX

Crystal structure of HLA-B*4001 in complex with SARS-CoV derived peptide N216-225 GETALALLLL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Salt bridge-forming residues positioned over viral peptides presented by MHC class I impacts T-cell recognition in a binding-dependent manner.

Ji, W.Niu, L.Peng, W.Zhang, Y.Cheng, H.Gao, F.Shi, Y.Qi, J.Gao, G.F.Liu, W.J.

(2019) Mol Immunol 112: 274-282

  • DOI: https://doi.org/10.1016/j.molimm.2019.06.005
  • Primary Citation of Related Structures:  
    6IEX

  • PubMed Abstract: 

    The viral peptides presentation by major histocompatibility complex class I (MHC I) molecules play a pivotal role in T-cell recognition and the subsequent virus clearance. This process is delicately adjusted by the variant residues of MHC I, especially the residues in the peptide binding groove (PBG). In a series of MHC I molecules, a salt bridge is formed above the N-terminus of the peptides. However, the potential impact of the salt bridge on peptide binding and T-cell receptor (TCR) recognition of MHC I, as well as the corresponding molecular basis, are still largely unknown. Herein, we determined the structures of HLA-B*4001 and H-2K d in which two different types of salt bridges (Arg62-Glu163 or Arg66-Glu163) across the PBG were observed. Although the two salt bridges led to different conformation shifts of both the MHC I α helix and the peptides, binding of the peptides with the salt bridge residues was relatively conserved. Furthermore, through a series of in vitro and in vivo investigations, we found that MHC I mutations that disrupt the salt bridge alleviate peptide binding and can weaken the TCR recognition of MHC I-peptide complexes. Our study may provide key references for understanding MHC I-restricted peptide recognition by T-cells.


  • Organizational Affiliation

    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 100052, China; School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China. Electronic address: liujun@ivdc.chinacdc.cn.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigen274Homo sapiensMutation(s): 0 
Gene Names: HLA-B
UniProt
Find proteins for A0A499S0B6 (Homo sapiens)
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Go to UniProtKB:  A0A499S0B6
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UniProt GroupA0A499S0B6
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
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PHAROS:  P61769
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
GLY-GLU-THR-ALA-LEU-ALA-LEU-LEU-LEU-LEU10Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: N9a
UniProt
Find proteins for P59595 (Severe acute respiratory syndrome coronavirus)
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Go to UniProtKB:  P59595
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UniProt GroupP59595
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.482α = 90
b = 69.274β = 90
c = 120.936γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2021-03-31
    Changes: Database references