Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 96.50 kDa 
• Atom Count: 6753 
• Residue Count: 803 
• Unique protein chains: 4

6CWE

Structure of alpha-GSA[8,6P] bound by CD1d and in complex with the Va14Vb8.2 TCR

• DOI: 10.2210/pdb6CWE/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda, Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2018-03-30 Released: 2019-04-03 
• Deposition Author(s): Wang, J., Zajonc, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.236 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

Glycolipid recognition by iNKT cells

Wang, J., Zajonc, D.

To be published.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d1	A	285	Mus musculus	Mutation(s): 0  Gene Names: Cd1d1, mCG_3074, Cd1.1
Find proteins for P11609 (Mus musculus) Explore P11609  Go to UniProtKB:  P11609

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	Mus musculus	Mutation(s): 0  Gene Names: B2m
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimeric T cell antigen receptor alpha chain Va14,Va24,Ja18	C	209	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimeric T cell antigen receptor beta chain Vb8.2, vb11	D	241	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F	3		N-Glycosylation

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7LP	A	(5R,6S,7S)-5,6-dihydroxy-7-(octanoylamino)-N-(6-phenylhexyl)-8-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octanamide C34 H58 N2 O10 GAPCJLRKOKSZTA-RMRXMYJTSA-N
PLM	A	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.236 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.18	α = 90
b = 190.168	β = 90
c = 150.965	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-03-30 
• Released Date: 2019-04-03 
Deposition Author(s): Wang, J., Zajonc, D.

Revision History 

• Version 1.0: 2019-04-03
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary