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: 46395.41 
• Atom Count: 3275 
• Residue Count: 384 
• Unique protein chains: 2

3T1F

Crystal structure of the mouse CD1d-Glc-DAG-s2 complex

• DOI: 10.2210/pdb3T1F/pdb

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


• Deposited: 2011-07-21 Released: 2011-09-21 
• Deposition Author(s): Girardi, E., Zajonc, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.219 
• R-Value Work: 0.187 

Literature

Invariant natural killer T cells recognize glycolipids from pathogenic Gram-positive bacteria.

Kinjo, Y., Illarionov, P., Vela, J.L., Pei, B., Girardi, E., Li, X., Li, Y., Imamura, M., Kaneko, Y., Okawara, A., Miyazaki, Y., Gomez-Velasco, A., Rogers, P., Dahesh, S., Uchiyama, S., Khurana, A., Kawahara, K., Yesilkaya, H., Andrew, P.W., Wong, C.H., Kawakami, K., Nizet, V., Besra, G.S., Tsuji, M., Zajonc, D.M., Kronenberg, M.

(2011) Nat.Immunol. 12: 966-974

• PubMed: 21892173 
• DOI: 10.1038/ni.2096


• PubMed Abstract: 
  

Natural killer T cells (NKT cells) recognize glycolipid antigens presented by CD1d. These cells express an evolutionarily conserved, invariant T cell antigen receptor (TCR), but the forces that drive TCR conservation have remained uncertain. Here we show that NKT cells recognized diacylglycerol-containing glycolipids from Streptococcus pneumoniae, the leading cause of community-acquired pneumonia, and group B Streptococcus, which causes neonatal sepsis and meningitis. Furthermore, CD1d-dependent responses by NKT cells were required for activation and host protection. The glycolipid response was dependent on vaccenic acid, which is present in low concentrations in mammalian cells. Our results show how microbial lipids position the sugar for recognition by the invariant TCR and, most notably, extend the range of microbes recognized by this conserved TCR to several clinically important bacteria.

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Organizational Affiliation: 

Division of Developmental Immunology, La Jolla Institute for Allergy & Immunology, La Jolla, California, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Antigen-presenting glycoprotein CD1d1	A	285	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
3TF	A	(2S)-1-(alpha-D-glucopyranosyloxy)-3-(hexadecanoyloxy)propan-2-yl (11Z)-octadec-11-enoate C43 H80 O10 FJAAFGBZVPKOCR-HBHGLPGMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.219 
• R-Value Work: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 42.191	α = 90.00
b = 107.381	β = 90.00
c = 110.305	γ = 90.00

Software Package:

Software Name	Purpose
Blu-Ice	data collection
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-07-21 
• Released Date: 2011-09-21 
• Deposition Author(s): Girardi, E., Zajonc, D.M.

Revision History 

• Version 1.0: 2011-09-21
  Type: Initial release
• Version 1.1: 2011-10-05
  Type: Database references