Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 47898.82 
• Atom Count: 3278 
• Residue Count: 386 
• Unique protein chains: 2

3GMP

Structure of mouse CD1d in complex with PBS-25

• DOI: 10.2210/pdb3GMP/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda


• Deposited: 2009-03-14 Released: 2009-11-10 
• Deposition Author(s): Schiefner, A., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.216 
• R-Value Work: 0.176 

Literature

Structural evaluation of potent NKT cell agonists: implications for design of novel stimulatory ligands.

Schiefner, A., Fujio, M., Wu, D., Wong, C.H., Wilson, I.A.

(2009) J.Mol.Biol. 394: 71-82

• PubMed: 19732779 
• DOI: 10.1016/j.jmb.2009.08.061
• Primary Citation of Related Structures:  
  3GMR, 3GMQ, 3GMO, 3GMN, 3GMM, 3GML


• PubMed Abstract: 
  

Natural killer T (NKT) cells are a subset of T cells that are activated by CD1d-glycolipid complexes through a semi-invariant alphabeta T cell receptor (NKT TCR). Upon activation, NKT cells secrete regulatory cytokines that are implicated in T helper cell responses. alpha-Galactosylceramide (alpha-GalCer) is a potent NKT cell agonist when presented by CD1d. Phenyl ring substitutions of the alpha-GalCer fatty acid moiety were recently found to be superior in eliciting regulatory cytokines. Crystal structures of four new mouse CD1d-lipid complexes (five structures), a new PBS-25 complex, and CD1d with an endogenous ligand, at 1.6-1.9 A resolution, reveal that the alpha-GalCer phenyl analogues impart minor structural differences to the A'-pocket, while the sphingosine and galactose moieties, important for NKT TCR recognition, remain virtually unchanged. The observed differences in cytokine-release profiles appear to be associated with increased stability of the CD1d-glycolipid complexes rather than increased affinity for the NKT TCR. Furthermore, comparison of mouse CD1d-glycolipid complexes in different crystallographic space groups reveals considerable conformational variation, particularly above the F'-pocket, the primary site of interaction with the NKT TCR. We propose that modifications of the sphingosine moiety or other substitutions that decrease alpha-GalCer flexibility would stabilize the F'-pocket. Such compounds might then increase CD1d affinity for the NKT TCR and further enhance the stimulatory and regulatory properties of alpha-GalCer derivatives.

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Organizational Affiliation: 

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
T-cell surface glycoprotein CD1d1	A	287	Mus musculus	Mutation(s): 0  Gene Names: Cd1d1 (Cd1.1)
Find proteins for P11609 (Mus musculus) Go to UniProtKB:  P11609

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Beta-2 microglobulin	B	99	Mus musculus	Mutation(s): 0  Gene Names: B2m
Find proteins for P01887 (Mus musculus) Go to UniProtKB:  P01887

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PBS	A	(2S,3S,4R)-N-OCTANOYL-1-[(ALPHA-D-GALACTOPYRANOSYL)OXY]-2-AMINO-OCTADECANE-3,4-DIOL C32 H63 N O9 PFXOKSFCNLTBGK-YFWOXBOYSA-N
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
FUC	A	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
EDO	A, B	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
BMA	A	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PLM	A	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.216 
• R-Value Work: 0.176 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 41.710	α = 90.00
b = 97.730	β = 106.52
c = 55.490	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
XDS	data reduction
MAR345	data collection
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-03-14 
• Released Date: 2009-11-10 
• Deposition Author(s): Schiefner, A., Wilson, I.A.

Revision History 

• Version 1.0: 2009-11-10
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Type: Refinement description