4L4V

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

• PDB DOI:  https://doi.org/10.2210/pdb4L4V/pdb

• Classification: Membrane Protein/Immune System
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2013-06-09 Released: 2013-07-17 
• Deposition Author(s): Patel, O., Kjer-Nielsen, L., Le Nours, J., Eckle, S.B.G., Birkinshaw, R.W., 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.

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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 

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

• PubMed: 23846752 
• 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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 188.25 kDa 
• Atom Count: 13,688 
• Modelled Residue Count: 1,584 
• Deposited Residue Count: 1,636 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major histocompatibility complex class I-related gene protein	A, C	271	Homo sapiens	Mutation(s): 1  Gene Names: MR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q95460 (Homo sapiens) Explore Q95460  Go to UniProtKB:  Q95460
PHAROS:  Q95460

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, F	99	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MAIT T-cell receptor alpha chain	D, G	203	Homo sapiens	Mutation(s): 0  Gene Names: TCR alpha, TRA@
UniProt
Find proteins for Q6P4G7 (Homo sapiens) Explore Q6P4G7  Go to UniProtKB:  Q6P4G7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
MAIT T-cell receptor beta chain	E, H	245	Homo sapiens	Mutation(s): 0  Gene Names: TCR beta, TRBC1
UniProt
Find proteins for P01850 (Homo sapiens) Explore P01850  Go to UniProtKB:  P01850

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1VY	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
GOL	J [auth B], K [auth B], M [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 218.37	α = 90
b = 71.203	β = 104.86
c = 144.642	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-17 
Deposition Author(s): Patel, O., Kjer-Nielsen, L., Le Nours, J., Eckle, S.B.G., Birkinshaw, R.W., 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.

Revision History  

• 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