4WWK

Crystal structure of human TCR Alpha Chain-TRAV12-3, Beta Chain-TRBV6-5, Antigen-presenting molecule CD1d, and Beta-2-microglobulin

PDB DOI: https://doi.org/10.2210/pdb4WWK/pdb

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

Deposited: 2014-11-11 Released: 2016-02-03
Deposition Author(s): Le Nours, J., Praveena, T., Pellicci, D.G., Gherardin, N.A., Lim, R.T., Besra, G., Keshipeddy, A., Richardson, S.K., Howell, A.R., Gras, S., Godfrey, D.I., Rossjohn, J., Uldrich, A.P.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.256
R-Value Work: 0.195
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 96.99 kDa
Atom Count: 5,883
Modelled Residue Count: 797
Deposited Residue Count: 849
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR Alpha Chain-TRAV12-3	A	209	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0B4J271 (Homo sapiens) Explore A0A0B4J271 Go to UniProtKB: A0A0B4J271
PHAROS: A0A0B4J271 GTEx: ENSG00000211794
Find proteins for P01848 (Homo sapiens) Explore P01848 Go to UniProtKB: P01848
PHAROS: P01848
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	A0A0B4J271P01848
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR Beta Chain-TRBV6-5	B	243	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for A0A5B9 (Homo sapiens) Explore A0A5B9 Go to UniProtKB: A0A5B9
PHAROS: A0A5B9
Find proteins for A0A0K0K1A5 (Homo sapiens) Explore A0A0K0K1A5 Go to UniProtKB: A0A0K0K1A5
PHAROS: A0A0K0K1A5 GTEx: ENSG00000211721
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	A0A5B9A0A0K0K1A5
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d	C	278	Homo sapiens	Mutation(s): 0 Gene Names: CD1D
UniProt & NIH Common Fund Data Resources
Find proteins for P15813 (Homo sapiens) Explore P15813 Go to UniProtKB: P15813
PHAROS: P15813 GTEx: ENSG00000158473
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15813
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	119	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JLS Query on JLS Download Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C]	G [auth C]	(15Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]tetracos-15-enamide C₄₈ H₉₃ N O₉ QMLKBWVXCMTWOZ-WWHSRKRPSA-N		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain F [auth C] MOL2 format, chain E [auth C] MOL2 format, chain F [auth C]	E [auth C], F [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth C] Focus chain F [auth C] Interactions & Density Focus chain E [auth C] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.256
R-Value Work: 0.195
R-Value Observed: 0.198
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.38	α = 90
b = 76.07	β = 90
c = 255.72	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-02-03

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2016-02-03
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Data collection, Derived calculations
Version 1.2: 2018-04-04
Changes: Data collection, Database references
Version 1.3: 2020-01-08
Changes: Author supporting evidence
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.5: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.6: 2024-03-13
Changes: Source and taxonomy