1G6R

A FUNCTIONAL HOT SPOT FOR ANTIGEN RECOGNITION IN A SUPERAGONIST TCR/MHC COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.298 

wwPDB Validation   3D Report Full Report


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


Literature

A functional hot spot for antigen recognition in a superagonist TCR/MHC complex.

Degano, M., Garcia, K.C., Apostolopoulos, V., Rudolph, M.G., Teyton, L., Wilson, I.A.

(2000) Immunity 12: 251-261

  • DOI: 10.1016/s1074-7613(00)80178-8
  • Primary Citation of Related Structures:  
    1G6R

  • PubMed Abstract: 

    • A longstanding question in T cell receptor signaling is how structurally similar ligands, with similar affinities, can have substantially different biological activity. The crystal structure of the 2C TCR complex of H-2Kb with superagonist peptide SIYR a ...

    A longstanding question in T cell receptor signaling is how structurally similar ligands, with similar affinities, can have substantially different biological activity. The crystal structure of the 2C TCR complex of H-2Kb with superagonist peptide SIYR at 2.8 A elucidates a structural basis for TCR discrimination of altered peptide ligands. The difference in antigen potency is modulated by two cavities in the TCR combining site, formed mainly by CDRs 3alpha, 3beta, and 1beta, that complement centrally located peptide residues. This "functional hot spot" allows the TCR to finely discriminate amongst energetically similar interactions within different ligands for those in which the peptide appropriately stabilizes the TCR/pMHC complex and provides a new structural perspective for understanding differential signaling resulting from T cell cross-reactivity.

    Related Citations: 
    • 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
    Organizational Affiliation: 

    Department of Molecular Biology and Skaggs Institute for Chemical Biology, La Jolla, California 92037, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA T CELL RECEPTOR A, C202Mus musculusMutation(s): 0 
Find proteins for P01738 (Mus musculus)
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Go to UniProtKB:  P01738
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BETA T CELL RECEPTOR B, D237Mus musculusMutation(s): 0 
Find proteins for P01852 (Mus musculus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE H, I274Mus musculusMutation(s): 0 
Gene Names: H2-K1, H2-K
Find proteins for P01901 (Mus musculus)
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Go to UniProtKB:  P01901
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-2 MICROGLOBULIN L, M99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC:  MGI:88127
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
SIYR PEPTIDE P, Q8N/AMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.298 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 297.71α = 90
b = 94.57β = 90
c = 84.89γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation