4N5E

42F3 TCR pCPA12/H-2Ld complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
42F3 alpha VmChC212Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Traj58
Find proteins for P01738 (Mus musculus)
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Go to UniProtKB:  P01738
Find proteins for P01848 (Homo sapiens)
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Go to UniProtKB:  P01848
NIH Common Fund Data Resources
PHAROS  P01848
Find proteins for A0A0G2JFA3 (Mus musculus)
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Go to UniProtKB:  A0A0G2JFA3
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
42F3 beta VmChD243Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Trbj2-2
Find proteins for A0A0A6YX08 (Mus musculus)
Explore A0A0A6YX08 
Go to UniProtKB:  A0A0A6YX08
Find proteins for A0A5B9 (Homo sapiens)
Explore A0A5B9 
Go to UniProtKB:  A0A5B9
NIH Common Fund Data Resources
PHAROS  A0A5B9
Find proteins for A0A075B5I3 (Mus musculus)
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Go to UniProtKB:  A0A075B5I3
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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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
pCPA12B9N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.57α = 90
b = 101.57β = 90
c = 327.13γ = 120
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: 2015-08-19
    Type: Initial release
  • Version 1.1: 2018-09-26
    Changes: Data collection, Database references