4MS8

42F3 TCR pCPB9/H-2Ld Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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:  
    4N0C, 4MS8, 4N5E, 4MVB, 4MXQ

  • 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

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
42F3 alphaC212Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
42F3 betaD243Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, L-D alpha chainA180Mus musculusMutation(s): 7 
Gene Names: H2-L
Find proteins for P01897 (Mus musculus)
Explore P01897 
Go to UniProtKB:  P01897
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
pCPB9B9N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.26α = 90
b = 60.62β = 96.06
c = 70.1γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2018-09-26
    Changes: Data collection, Database references