3NFN | pdb_00003nfn

Recognition of peptide-MHC by a V-delta/V-beta TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 
    0.222 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3NFN

This is version 1.2 of the entry. See complete history

Literature

Plasticity of human CD8 alpha 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 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.

Macromolecule Content 

  • Total Structure Weight: 44.72 kDa 
  • Atom Count: 3,386 
  • Modeled Residue Count: 384 
  • Deposited Residue Count: 384 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-24 alpha chain274Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04439
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
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)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
10-mer peptide from Protein Nef10Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q9YYU8 (Human immunodeficiency virus type 1)
Explore Q9YYU8 
Go to UniProtKB:  Q9YYU8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YYU8
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free:  0.222 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.735α = 90
b = 65.062β = 90.23
c = 50.415γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-13
    Type: Initial release
  • Version 1.1: 2013-09-11
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Structure summary