6W9U

Structure of human MAIT A-F7 TCR in complex with patient MR1-R9H-Ac-6-FP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Absence of mucosal-associated invariant T cells in a person with a homozygous point mutation in MR1 .

Howson, L.J.Awad, W.von Borstel, A.Lim, H.J.McWilliam, H.E.G.Sandoval-Romero, M.L.Majumdar, S.Hamzeh, A.R.Andrews, T.D.McDermott, D.H.Murphy, P.M.Le Nours, J.Mak, J.Y.W.Liu, L.Fairlie, D.P.McCluskey, J.Villadangos, J.A.Cook, M.C.Turner, S.J.Davey, M.S.Ojaimi, S.Rossjohn, J.

(2020) Sci Immunol 5

  • DOI: 10.1126/sciimmunol.abc9492
  • Primary Citation of Related Structures:  
    6W9U, 6W9V

  • PubMed Abstract: 
  • The role unconventional T cells play in protective immunity in humans is unclear. Mucosal-associated invariant T (MAIT) cells are an unconventional T cell subset restricted to the antigen-presenting molecule MR1. Here, we report the discovery of a pa ...

    The role unconventional T cells play in protective immunity in humans is unclear. Mucosal-associated invariant T (MAIT) cells are an unconventional T cell subset restricted to the antigen-presenting molecule MR1. Here, we report the discovery of a patient homozygous for a rare Arg31His (R9H in the mature protein) mutation in MR1 who has a history of difficult-to-treat viral and bacterial infections. MR1 R9H was unable to present the potent microbially derived MAIT cell stimulatory ligand. The MR1 R9H crystal structure revealed that the stimulatory ligand cannot bind due to the mutation lying within, and causing structural perturbation to, the ligand-binding domain of MR1. While MR1 R9H could bind and be up-regulated by a MAIT cell inhibitory ligand, the patient lacked circulating MAIT cells. This shows the importance of the stimulatory ligand for MAIT cell selection in humans. The patient had an expanded γδ T cell population, indicating a compensatory interplay between these unconventional T cell subsets.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major histocompatibility complex class I-related gene proteinAC271Homo sapiensMutation(s): 1 
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-microglobulinBF100Homo 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
TCR-alpha chainDG204Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
TCR-beta chainEH246Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TKG
Query on TKG

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A, C
1-[[6-(1-$l^{1}-oxidanylethyl)-4-$l^{3}-oxidanylidene-2,3,6,8~{a}-tetrahydropteridin-2-yl]-$l^{2}-azanyl]ethanone
C10 H9 N5 O3
OMULKSTUKAPZMF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A, C, F
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 218.317α = 90
b = 70.788β = 104.592
c = 142.983γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-03-23 
  • Released Date: 2020-08-05 
  • Deposition Author(s): Awad, W., Rossjohn, J.

Funding OrganizationLocationGrant Number
Australian Research Council (ARC)Australia--

Revision History 

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references