9BYS | pdb_00009bys

Structure of human MAIT BV28 TCR in complex with human MR1-5-OP-RU

• PDB DOI: https://doi.org/10.2210/pdb9BYS/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-24 Released: 2025-06-11 
• Deposition Author(s): Awad, W., Rossjohn, J.
• Funding Organization(s): Australian Research Council (ARC), National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.252 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Structure of human MAIT BV28 TCR in complex with human MR1-5-OP-RU

Awad, W., Rossjohn, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 94.92 kDa 
• Atom Count: 5,889 
• Modeled Residue Count: 735 
• Deposited Residue Count: 819 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major histocompatibility complex class I-related gene protein	A	271	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR beta chain	B [auth AAAB]	244	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR alpha chain	C [auth AAAC]	204	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	D [auth AAAD]	100	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 GTEx:  ENSG00000166710

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q87 (Subject of Investigation/LOI)	E [auth A]	1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol C12 H18 N4 O7 LXKLTDXEFFOBPT-CEKOQDAHSA-N
GOL	F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.252 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.35	α = 90
b = 111.35	β = 90
c = 206.46	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Awad, W., Rossjohn, J.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DE220101491
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release