2CKB | pdb_00002ckb

STRUCTURE OF THE 2C/KB/DEV8 COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.322 (Depositor) 
  • R-Value Work: 
    0.221 (Depositor) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis of plasticity in T cell receptor recognition of a self peptide-MHC antigen.

Garcia, K.C.Degano, M.Pease, L.R.Huang, M.Peterson, P.A.Teyton, L.Wilson, I.A.

(1998) Science 279: 1166-1172

  • DOI: https://doi.org/10.1126/science.279.5354.1166
  • Primary Citation of Related Structures:  
    2CKB

  • PubMed Abstract: 

    The T cell receptor (TCR) inherently has dual specificity. T cells must recognize self-antigens in the thymus during maturation and then discriminate between foreign pathogens in the periphery. A molecular basis for this cross-reactivity is elucidated by the crystal structure of the alloreactive 2C TCR bound to self peptide-major histocompatibility complex (pMHC) antigen H-2Kb-dEV8 refined against anisotropic 3.0 angstrom resolution x-ray data. The interface between peptide and TCR exhibits extremely poor shape complementarity, and the TCR beta chain complementarity-determining region 3 (CDR3) has minimal interaction with the dEV8 peptide. Large conformational changes in three of the TCR CDR loops are induced upon binding, providing a mechanism of structural plasticity to accommodate a variety of different peptide antigens. Extensive TCR interaction with the pMHC alpha helices suggests a generalized orientation that is mediated by the Valpha domain of the TCR and rationalizes how TCRs can effectively "scan" different peptides bound within a large, low-affinity MHC structural framework for those that provide the slight additional kinetic stabilization required for signaling.


  • Organizational Affiliation
    • Department of Molecular Biology and the Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA, BETA T CELL RECEPTORA,
F [auth C]
202Mus musculusMutation(s): 0 
UniProt
Find proteins for P01738 (Mus musculus)
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UniProt GroupP01738
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA, BETA T CELL RECEPTORB,
G [auth D]
237Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE K(B)C [auth H],
H [auth I]
274Mus musculusMutation(s): 0 
UniProt
Find proteins for P01901 (Mus musculus)
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UniProt GroupP01901
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DEV8 PEPTIDED [auth P],
I [auth Q]
8Mus musculusMutation(s): 0 
Gene Names: Ndufa4
UniProt
Find proteins for Q62425 (Mus musculus)
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UniProt GroupQ62425
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-2 MICROGLOBULINE [auth L],
J [auth M]
99Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
IMPC:  MGI:88127
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UniProt GroupP01887
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.322 (Depositor) 
  • R-Value Work:  0.221 (Depositor) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 295.66α = 90
b = 89.96β = 90
c = 84.12γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-04-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Data collection, Structure summary