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 6CPH | pdb_00006cph

Crystal structure of the F24 TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.233 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6CPH

This is version 1.3 of the entry. See complete history. 

Literature

CD4+T cell-mediated HLA class II cross-restriction in HIV controllers.

Galperin, M., Farenc, C., Mukhopadhyay, M., Jayasinghe, D., Decroos, A., Benati, D., Tan, L.L., Ciacchi, L., Reid, H.H., Rossjohn, J., Chakrabarti, L.A., Gras, S.

(2018) Sci Immunol 3

  • DOI: https://doi.org/10.1126/sciimmunol.aat0687
  • Primary Citation Related Structures: 
    6CPH, 6CPL, 6CPN, 6CPO, 6CQJ, 6CQL, 6CQN, 6CQQ, 6CQR

  • PubMed Abstract: 

    Rare individuals, termed HIV controllers, spontaneously control HIV infection by mounting efficient T cell responses against the virus. Protective CD4 + T cell responses from HIV controllers involve high-affinity public T cell receptors (TCRs) recognizing an immunodominant capsid epitope (Gag293) presented by a remarkably broad array of human leukocyte antigen (HLA) class II molecules. Here, we determine the structures of a prototypical public TCR bound to HLA-DR1, HLA-DR11, and HLA-DR15 molecules presenting the Gag293 epitope. TCR recognition was driven by contacts with the Gag293 epitope, a feature that underpinned the extensive HLA cross-restriction. These high-affinity TCRs promoted mature immunological synapse formation and cytotoxic capacity in both CD4 + and CD8 + T cells. The public TCRs suppressed HIV replication in multiple genetic backgrounds ex vivo, emphasizing the functional advantage conferred by broad HLA class II cross-restriction.


  • Organizational Affiliation: 
    • Pasteur Institute, Viral Pathogenesis Unit, Paris, France.

Macromolecule Content 

  • Total Structure Weight: 51.2 kDa 
  • Atom Count: 4,080 
  • Modeled Residue Count: 444 
  • Deposited Residue Count: 450 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TCR alpha chainA [auth D]205Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0B4J272 (Homo sapiens)
Explore A0A0B4J272 
Go to UniProtKB:  A0A0B4J272
PHAROS:  A0A0B4J272
GTEx:  ENSG00000211805 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B4J272
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TCR beta chainB [auth E]245Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for A0A5B9 (Homo sapiens)
Explore A0A5B9 
Go to UniProtKB:  A0A5B9
PHAROS:  A0A5B9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5B9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.233 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.124α = 90
b = 74.124β = 90
c = 193.244γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-06-27
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary