4G9F | pdb_00004g9f

Crystal Structure of C12C TCR-HLAB2705-KK10-L6M


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.238 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4G9F

This is version 1.4 of the entry. See complete history

Literature

A Molecular Basis for the Control of Preimmune Escape Variants by HIV-Specific CD8(+) T Cells.

Ladell, K.Hashimoto, M.Iglesias, M.C.Wilmann, P.G.McLaren, J.E.Gras, S.Chikata, T.Kuse, N.Fastenackels, S.Gostick, E.Bridgeman, J.S.Venturi, V.Arkoub, Z.A.Agut, H.van Bockel, D.J.Almeida, J.R.Douek, D.C.Meyer, L.Venet, A.Takiguchi, M.Rossjohn, J.Price, D.A.Appay, V.

(2013) Immunity 38: 425-436

  • DOI: https://doi.org/10.1016/j.immuni.2012.11.021
  • Primary Citation Related Structures: 
    4G8G, 4G8I, 4G9D, 4G9F

  • PubMed Abstract: 

    The capacity of the immune system to adapt to rapidly evolving viruses is a primary feature of effective immunity, yet its molecular basis is unclear. Here, we investigated protective HIV-1-specific CD8+ T cell responses directed against the immunodominant p24 Gag-derived epitope KK10 (KRWIILGLNK263-272) presented by human leukocyte antigen (HLA)-B∗2705. We found that cross-reactive CD8+ T cell clonotypes were mobilized to counter the rapid emergence of HIV-1 variants that can directly affect T cell receptor (TCR) recognition. These newly recruited clonotypes expressed TCRs that engaged wild-type and mutant KK10 antigens with similar affinities and almost identical docking modes, thereby accounting for their antiviral efficacy in HLA-B∗2705+ individuals. A protective CD8+ T cell repertoire therefore encompasses the capacity to control TCR-accessible mutations, ultimately driving the development of more complex viral escape variants that disrupt antigen presentation.


  • Organizational Affiliation
    • Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, Wales, UK.

Macromolecule Content 

  • Total Structure Weight: 96.27 kDa 
  • Atom Count: 7,375 
  • Modeled Residue Count: 840 
  • Deposited Residue Count: 840 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, B-27 alpha chain276Homo sapiensMutation(s): 0 
Gene Names: HLA-BHLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens)
Explore P01889 
Go to UniProtKB:  P01889
PHAROS:  P01889
GTEx:  ENSG00000234745 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01889
Sequence Annotations
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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)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Gag protein10Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
alpha chain C12C TCR204Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
beta chain C12C TCR250Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.238 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.406α = 90
b = 71.312β = 98.8
c = 109.566γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
SCALAdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-04-10
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Advisory, Refinement description
  • Version 1.3: 2020-04-22
    Changes: Database references, Structure summary
  • Version 1.4: 2024-11-27
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary