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 and generated by PISA (software)

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 194757.45 
• Atom Count: 12956 
• Residue Count: 1692 
• Unique protein chains: 4

3RUG

Crystal structure of Valpha10-Vbeta8.1 NKT TCR in complex with CD1d-alphaglucosylceramide (C20:2)

• DOI: 10.2210/pdb3RUG/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Trichoplusia ni, Escherichia coli


• Deposited: 2011-05-05 Released: 2011-08-03 
• Deposition Author(s): Patel, O., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.254 
• R-Value Work: 0.210 

Literature

A semi-invariant V(alpha)10(+) T cell antigen receptor defines a population of natural killer T cells with distinct glycolipid antigen-recognition properties

Uldrich, A.P., Patel, O., Cameron, G., Pellicci, D.G., Day, E.B., Sullivan, L.C., Kyparissoudis, K., Kjer-Nielsen, L., Vivian, J.P., Cao, B., Brooks, A.G., Williams, S.J., Illarionov, P., Besra, G.S., Turner, S.J., Porcelli, S.A., McCluskey, J., Smyth, M.J., Rossjohn, J., Godfrey, D.I.

(2011) Nat.Immunol. 12: 616-623

• PubMed: 21666690 
• DOI: 10.1038/ni.2051
• Primary Citation of Related Structures:  
  3AXL


• PubMed Abstract: 
  

Type I natural killer T cells (NKT cells) are characterized by an invariant variable region 14-joining region 18 (V(α)14-J(α)18) T cell antigen receptor (TCR) α-chain and recognition of the glycolipid α-galactosylceramide (α-GalCer) restricted to the antigen-presenting molecule CD1d. Here we describe a population of α-GalCer-reactive NKT cells that expressed a canonical V(α)10-J(α)50 TCR α-chain, which showed a preference for α-glucosylceramide (α-GlcCer) and bacterial α-glucuronic acid-containing glycolipid antigens. Structurally, despite very limited TCRα sequence identity, the V(α)10 TCR-CD1d-α-GlcCer complex had a docking mode similar to that of type I TCR-CD1d-α-GalCer complexes, although differences at the antigen-binding interface accounted for the altered antigen specificity. Our findings provide new insight into the structural basis and evolution of glycolipid antigen recognition and have notable implications for the scope and immunological role of glycolipid-specific T cell responses.

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Organizational Affiliation: 

Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Antigen-presenting glycoprotein CD1d1	A, C	302	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, D	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
Valpha10(mouse variable domain, human constant domain)	E, G	204	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Vbeta8.1(mouse variable domain, human constant domain)	F, H	241	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
DB6	A, C	(11E,14E)-N-[(2S,3S,4R)-1-(alpha-D-glucopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide C44 H83 N O9 WSXMIFGRYXQZQZ-IHVNXUITSA-N
NAG	A, C	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DB6	Kd: 4400 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.254 
• R-Value Work: 0.210 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 81.140	α = 90.00
b = 118.834	β = 110.24
c = 108.125	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-05 
• Released Date: 2011-08-03 
• Deposition Author(s): Patel, O., Rossjohn, J.

Revision History 

• Version 1.0: 2011-08-03
  Type: Initial release