Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 193240.09 
• Atom Count: 12204 
• Residue Count: 1668 
• Unique protein chains: 4

3TVM

Structure of the mouse CD1d-SMC124-iNKT TCR complex

• DOI: 10.2210/pdb3TVM/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Spodoptera frugiperda, Trichoplusia ni, Escherichia coli BL21(DE3)


• Deposited: 2011-09-20 Released: 2012-02-01 
• Deposition Author(s): Girardi, E., Li, Y., Zajonc, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.273 
• R-Value Work: 0.224 

Literature

Glycolipids that Elicit IFN-gama-Biased Responses from Natural Killer T Cells

Tyznik, A.J., Farber, E., Girardi, E., Birkholz, A., Li, Y., Chitale, S., So, R., Arora, P., Khurana, A., Wang, J., Porcelli, S.A., Zajonc, D.M., Kronenberg, M., Howell, A.R.

(2011) Chem.Biol. 18: 1620-1630

• PubMed: 22195564 
• DOI: 10.1016/j.chembiol.2011.10.015


• PubMed Abstract: 
  

Natural killer T (NKT) cells recognize glycolipids presented by CD1d. The first antigen described, α-galactosyl ceramide (αGalCer), is a potential anticancer agent whose activity depends upon IFN-γ secretion. We report two analogs of αGalCer based on a naturally occurring glycosphingolipid, plakoside A. These compounds induce enhanced IFN-γ that correlates with detergent-resistant binding to CD1d and an increased stability of the lipid-CD1d complexes on antigen-presenting cells. Structural analysis on one of the analogs indicates that it is more deeply bound inside the CD1d groove, suggesting tighter lipid-CD1d interactions. To our knowledge, this is the first example in which structural information provides an explanation for the increased lipid-CD1d stability, likely responsible for the Th1 bias. We provide insights into the mechanism of IFN-γ-inducing compounds, and because our compounds activate human NKT cells, they could have therapeutic utility.

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Organizational Affiliation: 

Division of Developmental Immunology, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Antigen-presenting glycoprotein CD1d1	A, E	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, F	99	Mus musculus	Mutation(s): 0  Gene Names: B2m
Find proteins for P01887 (Mus musculus) Go to UniProtKB:  P01887

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Valpha14 (mouse variable domain, human constant domain)	C, G	209	Homo sapiens	Mutation(s): 0  Gene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens) Go to UniProtKB:  P01848

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Vbeta8.2 (mouse variable domain, human constant domain)	D, H	241	Homo sapiens	Mutation(s): 0  Gene Names: TRBC2 (TCRBC2)
Find proteins for A0A5B9 (Homo sapiens) Go to UniProtKB:  A0A5B9

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
07P	A, E	N-[(2S,3R)-10-[(1R,2R)-2-decylcyclopropyl]-1-(alpha-D-galactopyranosyloxy)-3-hydroxydecan-2-yl]hexacosanamide SMC124 C55 H107 N O8 BCHXWZQXEKOXKQ-IYKQKVLOSA-N
CL	D	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL	E	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FUC	A, E	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
NAG	A, E	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: 0.273 
• R-Value Work: 0.224 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 78.970	α = 90.00
b = 150.570	β = 96.35
c = 101.960	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-09-20 
• Released Date: 2012-02-01 
• Deposition Author(s): Girardi, E., Li, Y., Zajonc, D.M.

Revision History 

• Version 1.0: 2012-02-01
  Type: Initial release