4F7C

Crystal structure of bovine CD1d with bound C12-di-sulfatide

• PDB DOI: https://doi.org/10.2210/pdb4F7C/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Bos taurus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-05-15 Released: 2012-11-14 
• Deposition Author(s): Wang, J., Zajonc, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 0.291 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 92.18 kDa 
• Atom Count: 6,216 
• Modelled Residue Count: 726 
• Deposited Residue Count: 762 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CD1D antigen, d polypeptide	A, C	283	Bos taurus	Mutation(s): 0  Gene Names: CD1D
UniProt
Find proteins for A1L565 (Bos taurus) Explore A1L565  Go to UniProtKB:  A1L565

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, D	98	Bos taurus	Mutation(s): 0  Gene Names: B2M
UniProt
Find proteins for P01888 (Bos taurus) Explore P01888  Go to UniProtKB:  P01888

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G31886NL GlyCosmos:  G31886NL GlyGen:  G31886NL

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0SG	I [auth A], J [auth C]	N-{(2S,3R,4E)-1-[(3,6-di-O-sulfo-beta-D-galactopyranosyl)oxy]-3-hydroxyoctadec-4-en-2-yl}dodecanamide C36 H69 N O14 S2 JBJSVLZKWGLXMO-AZNTWQPMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 0.291 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 
• Space Group: P 4₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.553	α = 90
b = 168.553	β = 90
c = 41.525	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Wang, J., Zajonc, D.M.

Revision History  

• Version 1.0: 2012-11-14
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary