4WW2

Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8, Beta Chain-TRBV7-8, Antigen-presenting glycoprotein CD1d, and Beta-2-microglobulin

• PDB DOI: https://doi.org/10.2210/pdb4WW2/pdb

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


• Deposited: 2014-11-10 Released: 2016-02-03 
• Deposition Author(s): Le Nours, J., Praveena, T., Pellicci, D., Gherardin, N.A., Lim, R.T., Besra, G., Keshipeddy, S., Richardson, S.K., Howell, A.R., Gras, S., Godfrey, D.I., Rossjohn, J., Uldrich, A.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.244 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 95.29 kDa 
• Atom Count: 6,540 
• Modelled Residue Count: 817 
• Deposited Residue Count: 833 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR Alpha Chain-TRAV21-TRAJ8	A	207	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01848 (Homo sapiens) Explore P01848  Go to UniProtKB:  P01848
PHAROS:  P01848
Find proteins for A0A0B4J279 (Homo sapiens) Explore A0A0B4J279  Go to UniProtKB:  A0A0B4J279
PHAROS:  A0A0B4J279 GTEx:  ENSG00000211801
UniProt Groups	P01848A0A0B4J279

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR Beta Chain-TRBV7-8	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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d	C	284	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 ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	D [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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JLS	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
NAG	E [auth C], F [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.244 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 209.99	α = 90
b = 46.3	β = 122.28
c = 124.65	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Le Nours, J., Praveena, T., Pellicci, D., Gherardin, N.A., Lim, R.T., Besra, G., Keshipeddy, S., Richardson, S.K., Howell, A.R., Gras, S., Godfrey, D.I., Rossjohn, J., Uldrich, A.P.

Revision History  

• Version 1.0: 2016-02-03
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Advisory, Data collection, Database references, Derived calculations
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-09-27
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary