Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

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

Macromolecule Content

• Total Structure Weight: 100.36 kDa 
• Atom Count: 6381 
• Residue Count: 782 
• 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
• Mutation(s): No 


• 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: 2.57 Å
• R-Value Free: 0.266 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 

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
• Primary Citation of Related Structures:  
  4EN3


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d	C	284	Homo sapiens	Mutation(s): 0  Gene Names: CD1D
Find proteins for P15813 (Homo sapiens) Explore P15813  Go to UniProtKB:  P15813
NIH Common Fund Data Resources
PHAROS  P15813 GTEx  ENSG00000158473

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN NKT TCR ALPHA CHAIN	A	220	Homo sapiens	Mutation(s): 0  Gene Names: B2M, HDCMA22P
Find proteins for K7N5M3 (Homo sapiens) Explore K7N5M3  Go to UniProtKB:  K7N5M3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN NKT TCR BETA CHAIN	B	259	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for K7N5M4 (Homo sapiens) Explore K7N5M4  Go to UniProtKB:  K7N5M4

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	D	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769 GTEx  ENSG00000166710

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
FUC	A	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
GOL	B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 0.266 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.112	α = 90
b = 72.573	β = 103.31
c = 113.747	γ = 90

Software Package:

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

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
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Advisory, Refinement description
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary