4L4V

Structure of human MAIT TCR in complex with human MR1-RL-6-Me-7-OH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Recognition of vitamin B metabolites by mucosal-associated invariant T cells.

Patel, O.Kjer-Nielsen, L.Le Nours, J.Eckle, S.B.Birkinshaw, R.Beddoe, T.Corbett, A.J.Liu, L.Miles, J.J.Meehan, B.Reantragoon, R.Sandoval-Romero, M.L.Sullivan, L.C.Brooks, A.G.Chen, Z.Fairlie, D.P.McCluskey, J.Rossjohn, J.

(2013) Nat Commun 4: 2142-2142

  • DOI: https://doi.org/10.1038/ncomms3142
  • Primary Citation of Related Structures:  
    4L4T, 4L4V

  • PubMed Abstract: 
  • The mucosal-associated invariant T-cell antigen receptor (MAIT TCR) recognizes MR1 presenting vitamin B metabolites. Here we describe the structures of a human MAIT TCR in complex with human MR1 presenting a non-stimulatory ligand derived from folic acid and an agonist ligand derived from a riboflavin metabolite ...

    The mucosal-associated invariant T-cell antigen receptor (MAIT TCR) recognizes MR1 presenting vitamin B metabolites. Here we describe the structures of a human MAIT TCR in complex with human MR1 presenting a non-stimulatory ligand derived from folic acid and an agonist ligand derived from a riboflavin metabolite. For both vitamin B antigens, the MAIT TCR docks in a conserved manner above MR1, thus acting as an innate-like pattern recognition receptor. The invariant MAIT TCR α-chain usage is attributable to MR1-mediated interactions that prise open the MR1 cleft to allow contact with the vitamin B metabolite. Although the non-stimulatory antigen does not contact the MAIT TCR, the stimulatory antigen does. This results in a higher affinity of the MAIT TCR for a stimulatory antigen in comparison with a non-stimulatory antigen. We formally demonstrate a structural basis for MAIT TCR recognition of vitamin B metabolites, while illuminating how TCRs recognize microbial metabolic signatures.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major histocompatibility complex class I-related gene protein
A, C
271Homo sapiensMutation(s): 1 
Gene Names: MR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q95460 (Homo sapiens)
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Go to UniProtKB:  Q95460
PHAROS:  Q95460
Entity Groups  
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UniProt GroupQ95460
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, F
99Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
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PHAROS:  P61769
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UniProt GroupP61769
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MAIT T-cell receptor alpha chain
D, G
203Homo sapiensMutation(s): 0 
Gene Names: TCR alphaTRA@
UniProt
Find proteins for Q6P4G7 (Homo sapiens)
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UniProt GroupQ6P4G7
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
MAIT T-cell receptor beta chain
E, H
245Homo sapiensMutation(s): 0 
Gene Names: TCR betaTRBC1
UniProt
Find proteins for P01850 (Homo sapiens)
Explore P01850 
Go to UniProtKB:  P01850
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UniProt GroupP01850
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1VY
Query on 1VY

Download Ideal Coordinates CCD File 
I [auth A],
L [auth C]
1-deoxy-1-(7-hydroxy-6-methyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol
C12 H16 N4 O7
COXMGTTXHPRZBO-BBVRLYRLSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth B],
K [auth B],
M [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1VY PDBBind:  4L4V Kd: 1650 (nM) from 1 assay(s)
Binding MOAD:  4L4V Kd: 1650 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 218.37α = 90
b = 71.203β = 104.86
c = 144.642γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-09-11
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description