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: 45485.34 
• Atom Count: 3157 
• Residue Count: 372 
• Unique protein chains: 2

1ZHN

Crystal Structure of mouse CD1d bound to the self ligand phosphatidylcholine

• DOI: 10.2210/pdb1ZHN/pdb

• Classification: IMMUNE SYSTEM MEMBRANE PROTEIN
• Organism(s): Mus musculus
• Expression System: Drosophila melanogaster


• Deposited: 2005-04-26 Released: 2005-07-19 
• Deposition Author(s): Giabbai, B., Sidobre, S., Crispin, M.M.D., Sanchez Ruiz, Y., Bachi, A., Kronenberg, M., Wilson, I.A., Degano, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.281 
• R-Value Work: 0.216 

Literature

Crystal structure of mouse CD1d bound to the self ligand phosphatidylcholine: a molecular basis for NKT cell activation

Giabbai, B., Sidobre, S., Crispin, M.M.D., Sanchez Ruiz, Y., Bachi, A., Kronenberg, M., Wilson, I.A., Degano, M.

(2005) J.Immunol. 175: 977-984

• PubMed: 16002697 
• DOI: 10.4049/jimmunol.175.2.977


• PubMed Abstract: 
  

NKT cells are immunoregulatory lymphocytes whose activation is triggered by the recognition of lipid Ags in the context of the CD1d molecules by the TCR. In this study we present the crystal structure to 2.8 A of mouse CD1d bound to phosphatidylcholine. The interactions between the ligand acyl chains and the CD1d molecule define the structural and chemical requirements for the binding of lipid Ags to CD1d. The orientation of the polar headgroup toward the C terminus of the alpha1 helix provides a rationale for the structural basis for the observed Valpha chain bias in invariant NKT cells. The contribution of the ligand to the protein surface suggests a likely mode of recognition of lipid Ags by the NKT cell TCR.

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Related Citations: 

• Crystal structure of mouse CD1: An MHC-like fold with a large hydrophobic binding groove
  Zeng, Z.,Castano, A.R.,Segelke, B.W.,Stura, E.A.,Peterson, P.A.,Wilson, I.A.
  (1997) Science 277: 339




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Organizational Affiliation: 

Biocrystallography Unit and Mass Spectrometry Unit, DIBIT San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CD1d1 antigen	A	273	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PC6	A	7-[(DODECANOYLOXY)METHYL]-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-3,5,8-TRIOXA-4-PHOSPHADOTRIACONTAN-1-AMINIUM 4-OXIDE C45 H90 N O8 P KWHAREAUZBVBDS-VZUYHUTRSA-N
GOL	B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
FUC	A	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.281 
• R-Value Work: 0.216 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 41.798	α = 90.00
b = 106.909	β = 90.00
c = 110.060	γ = 90.00

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-04-26 
• Released Date: 2005-07-19 
• Deposition Author(s): Giabbai, B., Sidobre, S., Crispin, M.M.D., Sanchez Ruiz, Y., Bachi, A., Kronenberg, M., Wilson, I.A., Degano, M.

Revision History 

• Version 1.0: 2005-07-19
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance