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: https://doi.org/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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA T CELL RECEPTORA,
F [auth C]
202Mus musculusMutation(s): 0 
UniProt
Find proteins for P01738 (Mus musculus)
Explore P01738 
Go to UniProtKB:  P01738
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01738
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BETA T CELL RECEPTORB,
G [auth D]
237Mus musculusMutation(s): 0 
UniProt
Find proteins for P01852 (Mus musculus)
Explore P01852 
Go to UniProtKB:  P01852
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01852
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULEC [auth H],
H [auth I]
274Mus musculusMutation(s): 0 
UniProt
Find proteins for P01901 (Mus musculus)
Explore P01901 
Go to UniProtKB:  P01901
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01901
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-2 MICROGLOBULIND [auth L],
I [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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01887
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
SIYR PEPTIDEE [auth P],
J [auth Q]
8N/AMutation(s): 0 
Sequence Annotations
Expand
  • 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

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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