9C42 | pdb_00009c42

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

PDB DOI: https://doi.org/10.2210/pdb9C42/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-06-02 Released: 2025-06-11
Deposition Author(s): Wang, C.J.H., Le Nours, J., Rossjohn, J.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free:
0.246 (Depositor), 0.246 (DCC)
R-Value Work:
0.194 (Depositor), 0.197 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Ellagic acid metabolism as a source of dietary MR1 ligands

Wang, C.J.H., Tang, J.S., Stephens, R., Faulkner, S., Gell, K., Li, Y., Cait, A., Rossjohn, J., Le Nours, J., Gasser, O.

To be published.

Macromolecule Content

Total Structure Weight: 189.27 kDa
Atom Count: 12,686
Modeled Residue Count: 1,611
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): 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q95460
Sequence Annotations Expand
Reference Sequence

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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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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TRA@ protein	D, G	204	Homo sapiens	Mutation(s): 0 Gene Names: TRA@
UniProt
Find proteins for Q6P4G7 (Homo sapiens) Explore Q6P4G7 Go to UniProtKB: Q6P4G7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6P4G7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
MAIT T-cell receptor beta chain	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
REF (Subject of Investigation/LOI) Query on REF 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]	2,3,7,8-tetrahydroxychromeno[5,4,3-cde]chromene-5,10-dione C₁₄ H₆ O₈ AFSDNFLWKVMVRB-UHFFFAOYSA-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 Q [auth E] SDF format, chain R [auth F] SDF format, chain S [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F] MOL2 format, chain S [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth F] mmCIF format, chain S [auth F]	Q [auth E], R [auth F], S [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth F] Interactions & Density Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth F]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain O [auth C] SDF format, chain P [auth D] MOL2 format, chain L [auth A] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] mmCIF format, chain L [auth A] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D]	L [auth A], O [auth C], P [auth D]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain O [auth C] Focus chain P [auth D] Interactions & Density Focus chain L [auth A] Focus chain O [auth C] Focus chain P [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain T [auth H] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain T [auth H] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain T [auth H]	J [auth A], K [auth A], T [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain T [auth H] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain T [auth H]