Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 100360.88 
• Atom Count: 6280 
• Residue Count: 863 
• Unique protein chains: 4

4EN3

Crystal structure of a human Valpha24(-) NKT TCR in complex with CD1d/alpha-galactosylceramide

• DOI: 10.2210/pdb4EN3/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni


• Deposited: 2012-04-12 Released: 2012-10-31 
• Deposition Author(s): Lopez-Sagaseta, J., Adams, E.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.568 Å
• R-Value Free: 0.266 
• R-Value Work: 0.208 

Literature

The Molecular Basis for Recognition of CD1d/alpha-Galactosylceramide by a Human Non-Valpha24 T Cell Receptor Struct. Title

Lopez-Sagaseta, J., Kung, J.E., Savage, P.B., Gumperz, J., Adams, E.J.

(2012) Plos Biol. 10: e1001412-e1001412

• PubMed: 23109910 
• DOI: 10.1371/journal.pbio.1001412


• PubMed Abstract: 
  

CD1d-mediated presentation of glycolipid antigens to T cells is capable of initiating powerful immune responses that can have a beneficial impact on many diseases. Molecular analyses have recently detailed the lipid antigen recognition strategies utilized by the invariant Vα24-Jα18 TCR rearrangements of iNKT cells, which comprise a subset of the human CD1d-restricted T cell population. In contrast, little is known about how lipid antigens are recognized by functionally distinct CD1d-restricted T cells bearing different TCRα chain rearrangements. Here we present crystallographic and biophysical analyses of α-galactosylceramide (α-GalCer) recognition by a human CD1d-restricted TCR that utilizes a Vα3.1-Jα18 rearrangement and displays a more restricted specificity for α-linked glycolipids than that of iNKT TCRs. Despite having sequence divergence in the CDR1α and CDR2α loops, this TCR employs a convergent recognition strategy to engage CD1d/αGalCer, with a binding affinity (∼2 µM) almost identical to that of an iNKT TCR used in this study. The CDR3α loop, similar in sequence to iNKT-TCRs, engages CD1d/αGalCer in a similar position as that seen with iNKT-TCRs, however fewer actual contacts are made. Instead, the CDR1α loop contributes important contacts to CD1d/αGalCer, with an emphasis on the 4'OH of the galactose headgroup. This is consistent with the inability of Vα24- T cells to respond to α-glucosylceramide, which differs from αGalCer in the position of the 4'OH. These data illustrate how fine specificity for a lipid containing α-linked galactose is achieved by a TCR structurally distinct from that of iNKT cells.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Antigen-presenting glycoprotein CD1d	C	284	Homo sapiens	Mutation(s): 0  Gene Names: CD1D
Find proteins for P15813 (Homo sapiens) Go to Gene View: CD1D Go to UniProtKB:  P15813

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
HUMAN NKT TCR ALPHA CHAIN	A	220	Homo sapiens	Mutation(s): 0  Gene Names: B2M
Find proteins for K7N5M3 (Homo sapiens) Go to Gene View: B2M Go to UniProtKB:  K7N5M3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
HUMAN NKT TCR BETA CHAIN	B	259	Homo sapiens	Mutation(s): 0  Gene Names: B2M
Find proteins for K7N5M4 (Homo sapiens) Go to Gene View: B2M Go to UniProtKB:  K7N5M4

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Beta-2-microglobulin	D	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M
Find proteins for P61769 (Homo sapiens) Go to Gene View: B2M Go to UniProtKB:  P61769

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FUC	A	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
AGH	C	N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE C50 H99 N O9 VQFKFAKEUMHBLV-BYSUZVQFSA-N
NAG	A, B, C	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.568 Å
• R-Value Free: 0.266 
• R-Value Work: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 57.112	α = 90.00
b = 72.573	β = 103.31
c = 113.747	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
DENZO	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-12 
• Released Date: 2012-10-31 
• Deposition Author(s): Lopez-Sagaseta, J., Adams, E.J.

Revision History 

• Version 1.0: 2012-10-31
  Type: Initial release
• Version 1.1: 2013-07-10
  Type: Database references
• Version 1.2: 2017-11-15
  Type: Advisory, Refinement description
• Version 1.3: 2018-01-24
  Type: Structure summary