5U72 | pdb_00005u72

Structure of human MR1-5OH-DCF in complex with human MAIT A-F7 TCR

PDB DOI: https://doi.org/10.2210/pdb5U72/pdb

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

Deposited: 2016-12-10 Released: 2017-02-08
Deposition Author(s): Keller, A.N., Rossjohn, J.
Funding Organization(s): Australian Research Council (ARC), National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.231 (Depositor), 0.230 (DCC)
R-Value Work:
0.173 (Depositor), 0.180 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

T-cell receptor complex

Keller, A.N., Rossjohn, J.

(2017) Nat Immunol

DOI: https://doi.org/10.1038/ni.3679

Macromolecule Content

Total Structure Weight: 187.97 kDa
Atom Count: 13,241
Modeled Residue Count: 1,600
Deposited Residue Count: 1,636
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, E [auth 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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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MAIT T-cell receptor alpha chain	B, F [auth D]	203	Homo sapiens	Mutation(s): 0 Gene Names: TRAV/TRAC
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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MAIT T-cell receptor beta chain	C [auth G], G [auth E]	245	Homo sapiens	Mutation(s): 0 Gene Names: TRBV/TRBC
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
Beta-2-microglobulin	D [auth H], H [auth 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 GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7ZV Query on 7ZV Download Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	5-hydroxydiclofenac C₁₄ H₁₁ Cl₂ N O₃ VNQURRWYKFZKJZ-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth F] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth F]	I [auth A], J [auth A], N [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth F] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.231 (Depositor), 0.230 (DCC)
R-Value Work: 0.173 (Depositor), 0.180 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 213.09	α = 90
b = 69.6	β = 103.72
c = 142.37	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-02-08

Deposition Author(s):

Keller, A.N.

Rossjohn, J.

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	CE140100011
National Health and Medical Research Council (NHMRC, Australia)	Australia	AF50

Revision History (Full details and data files)

Version 1.0: 2017-02-08
Type: Initial release
Version 1.1: 2017-09-13
Changes: Author supporting evidence, Data collection
Version 1.2: 2017-11-22
Changes: Refinement description
Version 1.3: 2018-01-17
Changes: Author supporting evidence
Version 1.4: 2020-01-01
Changes: Author supporting evidence
Version 1.5: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.6: 2024-11-20
Changes: Structure summary