4EN3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 ?
  • R-Value Free: 0.266 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.7 of the entry. See complete history


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

  • DOI: https://doi.org/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 V¦Á24-J¦Á18 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 TCR¦Á chain rearrangements. Here we present crystallographic and biophysical analyses of ¦Á-galactosylceramide (¦Á-GalCer) recognition by a human CD1d-restricted TCR that utilizes a V¦Á3.1-J¦Á18 rearrangement and displays a more restricted specificity for ¦Á-linked glycolipids than that of iNKT TCRs. Despite having sequence divergence in the CDR1¦Á and CDR2¦Á loops, this TCR employs a convergent recognition strategy to engage CD1d/¦ÁGalCer, with a binding affinity (¡«2 ?M) almost identical to that of an iNKT TCR used in this study. The CDR3¦Á loop, similar in sequence to iNKT-TCRs, engages CD1d/¦ÁGalCer in a similar position as that seen with iNKT-TCRs, however fewer actual contacts are made. Instead, the CDR1¦Á loop contributes important contacts to CD1d/¦ÁGalCer, with an emphasis on the 4'OH of the galactose headgroup. This is consistent with the inability of V¦Á24- T cells to respond to ¦Á-glucosylceramide, which differs from ¦ÁGalCer in the position of the 4'OH. These data illustrate how fine specificity for a lipid containing ¦Á-linked galactose is achieved by a TCR structurally distinct from that of iNKT cells.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1dA [auth C]284Homo sapiensMutation(s): 0 
Gene Names: CD1D
UniProt & NIH Common Fund Data Resources
Find proteins for P15813 (Homo sapiens)
Explore P15813 
Go to UniProtKB:  P15813
PHAROS:  P15813
GTEx:  ENSG00000158473 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15813
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HUMAN NKT TCR ALPHA CHAINB [auth A]220Homo sapiensMutation(s): 0 
UniProt
Find proteins for K7N5M3 (Homo sapiens)
Explore K7N5M3 
Go to UniProtKB:  K7N5M3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK7N5M3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HUMAN NKT TCR BETA CHAINC [auth B]259Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt
Find proteins for K7N5M4 (Homo sapiens)
Explore K7N5M4 
Go to UniProtKB:  K7N5M4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK7N5M4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGH
Query on AGH

Download Ideal Coordinates CCD File 
H [auth C]N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE
C50 H99 N O9
VQFKFAKEUMHBLV-BYSUZVQFSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth C],
F [auth C],
G [auth C],
J [auth A],
L [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
FUC
Query on FUC

Download Ideal Coordinates CCD File 
I [auth A]alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth B],
M [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 ?
  • R-Value Free: 0.266 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( ? )Angle ( ? )
a = 57.112¦Á = 90
b = 72.573¦Â = 103.31
c = 113.747¦Ã = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.5: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.6: 2023-12-27
    Changes: Derived calculations
  • Version 1.7: 2024-10-30
    Changes: Structure summary
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