9O05 | pdb_00009o05

Structure of human MAIT A-F7 TCR in complex with human MR1-riboflavin

PDB DOI: https://doi.org/10.2210/pdb9O05/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-04-02 Released: 2025-11-19
Deposition Author(s): Abdelaal, M., Rossjohn, J., Awad, W.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.201 (Depositor), 0.201 (DCC)
R-Value Work:
0.164 (Depositor), 0.165 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Major histocompatibility complex class I-related gene protein / TCR alpha /TCR beta / Beta-2-microglobulin complex

Abdelaal, M., Rossjohn, J., Awad, W.

To be published.

Macromolecule Content

Total Structure Weight: 189.58 kDa
Atom Count: 14,760
Modeled Residue Count: 1,606
Deposited Residue Count: 1,642
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

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 GTEx: ENSG00000153029
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q95460
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, F	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR-alpha	D, G	204	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR-beta	E, H	246	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RBF (Subject of Investigation/LOI) Query on RBF Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth C] MOL2 format, chain I [auth A] MOL2 format, chain M [auth C] mmCIF format, chain I [auth A] mmCIF format, chain M [auth C]	I [auth A], M [auth C]	RIBOFLAVIN C₁₇ H₂₀ N₄ O₆ AUNGANRZJHBGPY-SCRDCRAPSA-N		Interactions Focus chain I [auth A] Focus chain M [auth C] Interactions & Density Focus chain I [auth A] Focus chain M [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain O [auth C] SDF format, chain P [auth E] SDF format, chain Q [auth F] SDF format, chain R [auth F] SDF format, chain S [auth G] MOL2 format, chain K [auth A] MOL2 format, chain O [auth C] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth F] MOL2 format, chain S [auth G] mmCIF format, chain K [auth A] mmCIF format, chain O [auth C] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth F] mmCIF format, chain S [auth G]	K [auth A] O [auth C] P [auth E] Q [auth F] R [auth F] K [auth A], O [auth C], P [auth E], Q [auth F], R [auth F], S [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain O [auth C] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth G] Interactions & Density Focus chain K [auth A] Focus chain O [auth C] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth G]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth C] MOL2 format, chain J [auth A] MOL2 format, chain N [auth C] mmCIF format, chain J [auth A] mmCIF format, chain N [auth C]	J [auth A], N [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain N [auth C] Interactions & Density Focus chain J [auth A] Focus chain N [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain T [auth H] MOL2 format, chain T [auth H] mmCIF format, chain T [auth H]	T [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain T [auth H] Interactions & Density Focus chain T [auth H]