4N0C

42F3 TCR pCPE3/H-2Ld complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity.

Adams, J.J.Narayanan, S.Birnbaum, M.E.Sidhu, S.S.Blevins, S.J.Gee, M.H.Sibener, L.V.Baker, B.M.Kranz, D.M.Garcia, K.C.

(2016) Nat. Immunol. 17: 87-94

  • DOI: 10.1038/ni.3310
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The T cell antigen receptor (TCR)-peptide-major histocompatibility complex (MHC) interface is composed of conserved and diverse regions, yet the relative contribution of each in shaping recognition by T cells remains unclear. Here we isolated cross-r ...

    The T cell antigen receptor (TCR)-peptide-major histocompatibility complex (MHC) interface is composed of conserved and diverse regions, yet the relative contribution of each in shaping recognition by T cells remains unclear. Here we isolated cross-reactive peptides with limited homology, which allowed us to compare the structural properties of nine peptides for a single TCR-MHC pair. The TCR's cross-reactivity was rooted in highly similar recognition of an apical 'hot-spot' position in the peptide with tolerance of sequence variation at ancillary positions. Furthermore, we found a striking structural convergence onto a germline-mediated interaction between the TCR CDR1α region and the MHC α2 helix in twelve TCR-peptide-MHC complexes. Our studies suggest that TCR-MHC germline-mediated constraints, together with a focus on a small peptide hot spot, might place limits on peptide antigen cross-reactivity.


    Organizational Affiliation

    Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Howard Hughes Medical Institute, and Departments of Molecular and Cellular Physiology, and Structural Biology, Program in Immunology, Stanford University School of Medicine, Stanford, California, USA.,Department of Chemistry &Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA.,Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Terrence Donnelly Centre for Cellular &Biomolecular Research, Toronto, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 class I histocompatibility antigen, L-D alpha chain
A, E
180Mus musculusMutation(s): 7 
Gene Names: H2-L
Find proteins for P01897 (Mus musculus)
Go to UniProtKB:  P01897
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
pCPE3
B, F
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
42F3 VmCh alpha
C, G
212Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Traj58, TRAC (TCRA)
Find proteins for P01738 (Mus musculus)
Go to UniProtKB:  P01738
Find proteins for A0A0G2JFA3 (Mus musculus)
Go to UniProtKB:  A0A0G2JFA3
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
42F3 VmCh beta
D, H
243Homo sapiensMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: TRBC2 (TCRBC2), Trbv13-1, Trbj2-2
Find proteins for A0A5B9 (Homo sapiens)
Go to UniProtKB:  A0A5B9
Find proteins for A0A075B5I3 (Mus musculus)
Go to UniProtKB:  A0A075B5I3
Find proteins for A0A0A6YX08 (Mus musculus)
Go to UniProtKB:  A0A0A6YX08
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.192 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 102.450α = 90.00
b = 102.450β = 90.00
c = 325.660γ = 120.00
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
MOSFLMdata reduction
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2018-09-26
    Type: Data collection, Database references