3RDT

Crystal Structure of 809.B5 TCR complexed with MHC Class II I-Ab/3k peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A role for differential variable gene pairing in creating T cell receptors specific for unique major histocompatibility ligands.

Stadinski, B.D.Trenh, P.Smith, R.L.Bautista, B.Huseby, P.G.Li, G.Stern, L.J.Huseby, E.S.

(2011) Immunity 35: 694-704

  • DOI: 10.1016/j.immuni.2011.10.012
  • Primary Citation of Related Structures:  
    3RDT

  • PubMed Abstract: 
  • A limited set of T cell receptor (TCR) variable (V) gene segments are used to create a repertoire of TCRs that recognize all major histocompatibility complex (MHC) ligands within a species. How individual αβTCRs are constructed to specifically recognize a limited set of MHC ligands is unclear ...

    A limited set of T cell receptor (TCR) variable (V) gene segments are used to create a repertoire of TCRs that recognize all major histocompatibility complex (MHC) ligands within a species. How individual αβTCRs are constructed to specifically recognize a limited set of MHC ligands is unclear. Here we have identified a role for the differential pairing of particular V gene segments in creating TCRs that recognized MHC class II ligands exclusively, or cross-reacted with classical and nonclassical MHC class I ligands. Biophysical and structural experiments indicated that TCR specificity for MHC ligands is not driven by germline-encoded pairwise interactions.Rather, identical TCRβ chains can have altered peptide-MHC (pMHC) binding modes when paired with different TCRα chains. The ability of TCR chain pairing to modify how V region residues interact with pMHC helps to explain how the same V genes are used to create TCRs specific for unique MHC ligands.


    Organizational Affiliation

    Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class II histocompatibility antigen, A-B alpha chainA [auth C]182Mus musculusMutation(s): 0 
Gene Names: H2-Aa
UniProt
Find proteins for P14434 (Mus musculus)
Explore P14434 
Go to UniProtKB:  P14434
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
3K peptide, linker and MHC H-2 class II I-Ab beta chainB [auth D]217synthetic constructMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: H2-Ab1
UniProt
Find proteins for P14483 (Mus musculus)
Explore P14483 
Go to UniProtKB:  P14483
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
TCR 809.B5 alpha chainC [auth A]205Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
TCR 809.B5 beta chainD [auth B]241Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 239.855α = 90
b = 73.016β = 90.71
c = 65.669γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2012-02-08
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Refinement description, Source and taxonomy