3QZW

Plasticity of human CD8 binding to peptide-HLA-A*2402


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

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This is version 1.2 of the entry. See complete history


Literature

Plasticity of human CD8alpha alpha binding to peptide-HLA-A*2402

Shi, Y.Qi, J.Iwamoto, A.Gao, G.F.

(2011) Mol Immunol 48: 2198-2202

  • DOI: https://doi.org/10.1016/j.molimm.2011.05.009
  • Primary Citation of Related Structures:  
    3NFN, 3QZW

  • PubMed Abstract: 

    The human CD8 functions as a co-receptor for specific T cell recognition, and only one complex structure of human CD8αα binding to HLA-A*0201 has been solved, revealing the molecular basis of CD8 interacting with its ligand pHLA. Here, we present the complex structures of human CD8αα bound to HLA-A*2402, which demonstrate two opposite α3 domain CD loop shifts (either pull or push) in the HLA heavy chain upon CD8 engagement. Taking the previously reported mouse CD8-pMHC complex structures into account, from the structural view, all of the data indicate the plasticity of CD8 binding to pMHC/HLA, which facilitates its co-receptor function for T cells. The plasticity of CD8 binding appears not to affect the specificity of TCR recognition, as no peptide conformation change extends to the pMHC interface for TCR contacting.


  • Organizational Affiliation

    CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-24 alpha chain
A, D
274Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
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Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
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UniProt GroupP04439
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, E
100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
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PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
10-mer peptide from Protein Nef
C, F
10Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q9YYU8 (Human immunodeficiency virus 1)
Explore Q9YYU8 
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UniProt GroupQ9YYU8
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD8 alpha chain
G, H, I, J
114Homo sapiensMutation(s): 0 
Gene Names: CD8AMAL
UniProt & NIH Common Fund Data Resources
Find proteins for P01732 (Homo sapiens)
Explore P01732 
Go to UniProtKB:  P01732
PHAROS:  P01732
GTEx:  ENSG00000153563 
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UniProt GroupP01732
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.239α = 73.71
b = 67.019β = 71.84
c = 101.144γ = 81.43
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-07-03
    Changes: Database references