5D7L | pdb_00005d7l

Structure of human MR1-5-OP-RU in complex with human MAV36 TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.337 (Depositor), 0.340 (DCC) 
  • R-Value Work: 
    0.280 (Depositor), 0.285 (DCC) 
  • R-Value Observed: 
    0.283 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Diversity of T Cells Restricted by the MHC Class I-Related Molecule MR1 Facilitates Differential Antigen Recognition.

Gherardin, N.A.Keller, A.N.Woolley, R.E.Le Nours, J.Ritchie, D.S.Neeson, P.J.Birkinshaw, R.W.Eckle, S.B.Waddington, J.N.Liu, L.Fairlie, D.P.Uldrich, A.P.Pellicci, D.G.McCluskey, J.Godfrey, D.I.Rossjohn, J.

(2016) Immunity 44: 32-45

  • DOI: https://doi.org/10.1016/j.immuni.2015.12.005
  • Primary Citation Related Structures: 
    5D5M, 5D7I, 5D7J, 5D7K, 5D7L

  • PubMed Abstract: 

    A characteristic of mucosal-associated invariant T (MAIT) cells is the expression of TRAV1-2(+) T cell receptors (TCRs) that are activated by riboflavin metabolite-based antigens (Ag) presented by the MHC-I related molecule, MR1. Whether the MR1-restricted T cell repertoire and associated Ag responsiveness extends beyond these cells remains unclear. Here, we describe MR1 autoreactivity and folate-derivative reactivity in a discrete subset of TRAV1-2(+) MAIT cells. This recognition was attributable to CDR3β loop-mediated effects within a consensus TRAV1-2(+) TCR-MR1-Ag footprint. Furthermore, we have demonstrated differential folate- and riboflavin-derivative reactivity by a diverse population of "atypical" TRAV1-2(-) MR1-restricted T cells. We have shown that TRAV1-2(-) T cells are phenotypically heterogeneous and largely distinct from TRAV1-2(+) MAIT cells. A TRAV1-2(-) TCR docks more centrally on MR1, thereby adopting a markedly different molecular footprint to the TRAV1-2(+) TCR. Accordingly, diversity within the MR1-restricted T cell repertoire leads to differing MR1-restricted Ag specificity.


  • Organizational Affiliation
    • Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia; Cancer Immunology Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia.

Macromolecule Content 

  • Total Structure Weight: 188.77 kDa 
  • Atom Count: 12,574 
  • Modeled Residue Count: 1,550 
  • Deposited Residue Count: 1,634 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Major histocompatibility complex class I-related gene protein
A, C
271Homo sapiensMutation(s): 0 
Gene Names: MR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q95460 (Homo sapiens)
Explore Q95460 
Go to UniProtKB:  Q95460
PHAROS:  Q95460
GTEx:  ENSG00000153029 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ95460
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, F
100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
MAV36 TCR Alpha Chain
D, G
203Homo sapiensMutation(s): 0 
Gene Names: TRAV/TRAV
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
MAV36 TCR Beta Chain
E, H
243Homo sapiensMutation(s): 0 
Gene Names: TRBV/TRBC

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2LJ

Query on 2LJ



Download:Ideal Coordinates CCD File
I [auth A],
J [auth C]
1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol
C12 H20 N4 O6
YCMPUNANLDFPQG-FHZGFTDOSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.337 (Depositor), 0.340 (DCC) 
  • R-Value Work:  0.280 (Depositor), 0.285 (DCC) 
  • R-Value Observed: 0.283 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.28α = 90
b = 222.432β = 100.15
c = 98.979γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-02-03
    Changes: Database references
  • Version 2.0: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary
  • Version 2.1: 2024-10-23
    Changes: Structure summary