6CQR | pdb_00006cqr

Crystal structure of F24 TCR -DR1-RQ13 peptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 
    0.254 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 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: 191.95 kDa 
  • Atom Count: 13,648 
  • Modeled Residue Count: 1,655 
  • Deposited Residue Count: 1,670 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chain
A, F
182Homo sapiensMutation(s): 0 
Gene Names: HLA-DRAHLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens)
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PHAROS:  P01903
GTEx:  ENSG00000204287 
Entity Groups
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UniProt GroupP01903
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01903-1
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DRB1-1 beta chain
B, G
190Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens)
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Go to UniProtKB:  P01911
PHAROS:  P01911
GTEx:  ENSG00000196126 
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UniProt GroupP01911
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptide from Capsid protein p24
C, H
13HIV-1 M:B_HXB2RMutation(s): 0 
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
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UniProt GroupP04585
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
F24 alpha chain
D, I
205Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0B4J272 (Homo sapiens)
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PHAROS:  A0A0B4J272
GTEx:  ENSG00000211805 
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UniProt GroupA0A0B4J272
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
F24 beta chain
E, J
245Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for A0A5B9 (Homo sapiens)
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PHAROS:  A0A5B9
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UniProt GroupA0A5B9
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free:  0.254 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.929α = 90
b = 155.325β = 90
c = 133.14γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Derived calculations
  • Version 1.2: 2018-06-27
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-10-23
    Changes: Structure summary