4IIQ

Crystal structure of a human MAIT TCR in complex with bovine MR1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The molecular basis for Mucosal-Associated Invariant T cell recognition of MR1 proteins.

Lopez-Sagaseta, J.Dulberger, C.L.Crooks, J.E.Parks, C.D.Luoma, A.M.McFedries, A.Van Rhijn, I.Saghatelian, A.Adams, E.J.

(2013) Proc Natl Acad Sci U S A 110: E1771-E1778

  • DOI: 10.1073/pnas.1222678110
  • Primary Citation of Related Structures:  
    4IIQ

  • PubMed Abstract: 
  • Mucosal-associated invariant T (MAIT) cells are an evolutionarily conserved αβ T-cell lineage that express a semi-invariant T-cell receptor (TCR) restricted to the MHC related-1 (MR1) protein. MAIT cells are dependent upon MR1 expression and exposure ...

    Mucosal-associated invariant T (MAIT) cells are an evolutionarily conserved αβ T-cell lineage that express a semi-invariant T-cell receptor (TCR) restricted to the MHC related-1 (MR1) protein. MAIT cells are dependent upon MR1 expression and exposure to microbes for their development and stimulation, yet these cells can exhibit microbial-independent stimulation when responding to MR1 from different species. We have used this microbial-independent, cross-species reactivity of MAIT cells to define the molecular basis of MAIT-TCR/MR1 engagement and present here a 2.85 Å complex structure of a human MAIT-TCR bound to bovine MR1. The MR1 binding groove is similar in backbone structure to classical peptide-presenting MHC class I molecules (MHCp), yet is partially occluded by large aromatic residues that form cavities suitable for small ligand presentation. The docking of the MAIT-TCR on MR1 is perpendicular to the MR1 surface and straddles the MR1 α1 and α2 helices, similar to classical αβ TCR engagement of MHCp. However, the MAIT-TCR contacts are dominated by the α-chain, focused on the MR1 α2 helix. TCR β-chain contacts are mostly through the variable CDR3β loop that is positioned proximal to the CDR3α loop directly over the MR1 open groove. The elucidation of the MAIT TCR/MR1 complex structure explains how the semi-invariant MAIT-TCR engages the nonpolymorphic MR1 protein, and sheds light onto ligand discrimination by this cell type. Importantly, this structure also provides a critical link in our understanding of the evolution of αβ T-cell recognition of MHC and MHC-like ligands.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Human Mucosal Associated Invariant T cell receptor alpha chainA205Homo sapiensMutation(s): 0 
Gene Names: TRA@
Find proteins for Q6P4G7 (Homo sapiens)
Explore Q6P4G7 
Go to UniProtKB:  Q6P4G7
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Human Mucosal Associated Invariant T cell receptor beta chainB253Homo sapiensMutation(s): 0 
Gene Names: TRBC1
Find proteins for P01850 (Homo sapiens)
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Go to UniProtKB:  P01850
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulin, MHC class I-related proteinC392Bos taurusMutation(s): 0 
Gene Names: MR1Bt.63045
Find proteins for P01888 (Bos taurus)
Explore P01888 
Go to UniProtKB:  P01888
Find proteins for C1ITJ8 (Bos taurus)
Explore C1ITJ8 
Go to UniProtKB:  C1ITJ8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KFP
Query on KFP
CD-PEPTIDE LINKINGC13 H19 N7 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.045α = 90
b = 87.41β = 90
c = 156.372γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-05-01
    Changes: Database references
  • Version 1.2: 2013-05-29
    Changes: Database references
  • Version 1.3: 2017-08-23
    Changes: Source and taxonomy