6MWR

Recognition of MHC-like molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A class of gamma delta T cell receptors recognize the underside of the antigen-presenting molecule MR1.

Le Nours, J.Gherardin, N.A.Ramarathinam, S.H.Awad, W.Wiede, F.Gully, B.S.Khandokar, Y.Praveena, T.Wubben, J.M.Sandow, J.J.Webb, A.I.von Borstel, A.Rice, M.T.Redmond, S.J.Seneviratna, R.Sandoval-Romero, M.L.Li, S.Souter, M.N.T.Eckle, S.B.G.Corbett, A.J.Reid, H.H.Liu, L.Fairlie, D.P.Giles, E.M.Westall, G.P.Tothill, R.W.Davey, M.S.Berry, R.Tiganis, T.McCluskey, J.Pellicci, D.G.Purcell, A.W.Uldrich, A.P.Godfrey, D.I.Rossjohn, J.

(2019) Science 366: 1522-1527

  • DOI: 10.1126/science.aav3900
  • Primary Citation of Related Structures:  
    6MWR

  • PubMed Abstract: 
  • T cell receptors (TCRs) recognize antigens presented by major histocompatibility complex (MHC) and MHC class I-like molecules. We describe a diverse population of human γδ T cells isolated from peripheral blood and tissues that exhibit autoreactivity ...

    T cell receptors (TCRs) recognize antigens presented by major histocompatibility complex (MHC) and MHC class I-like molecules. We describe a diverse population of human γδ T cells isolated from peripheral blood and tissues that exhibit autoreactivity to the monomorphic MHC-related protein 1 (MR1). The crystal structure of a γδTCR-MR1-antigen complex starkly contrasts with all other TCR-MHC and TCR-MHC-I-like complex structures. Namely, the γδTCR binds underneath the MR1 antigen-binding cleft, where contacts are dominated by the MR1 α3 domain. A similar pattern of reactivity was observed for diverse MR1-restricted γδTCRs from multiple individuals. Accordingly, we simultaneously report MR1 as a ligand for human γδ T cells and redefine the parameters for TCR recognition.


    Organizational Affiliation

    Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major histocompatibility complex class I-related gene proteinA271Homo sapiensMutation(s): 0 
Gene Names: MR1
Find proteins for Q95460 (Homo sapiens)
Explore Q95460 
Go to UniProtKB:  Q95460
NIH Common Fund Data Resources
PHAROS  Q95460
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB99Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
G7 Gamma chain T cell receptorC244Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Delta chain of T cell receptorD236Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2LJ
Query on 2LJ

Download CCD File 
A
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
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
D
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.39α = 90
b = 88.39β = 90
c = 257.15γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary