4WW2 | pdb_00004ww2

Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8, Beta Chain-TRBV7-8, Antigen-presenting glycoprotein CD1d, and Beta-2-microglobulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 
    0.244 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.196 (Depositor) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4WW2

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Atypical natural killer T-cell receptor recognition of CD1d-lipid antigens.

Le Nours, J.Praveena, T.Pellicci, D.G.Gherardin, N.A.Ross, F.J.Lim, R.T.Besra, G.S.Keshipeddy, S.Richardson, S.K.Howell, A.R.Gras, S.Godfrey, D.I.Rossjohn, J.Uldrich, A.P.

(2016) Nat Commun 7: 10570-10570

  • DOI: https://doi.org/10.1038/ncomms10570
  • Primary Citation Related Structures: 
    4WW1, 4WW2, 4WWK

  • PubMed Abstract: 

    Crucial to Natural Killer T (NKT) cell function is the interaction between their T-cell receptor (TCR) and CD1d-antigen complex. However, the diversity of the NKT cell repertoire and the ensuing interactions with CD1d-antigen remain unclear. We describe an atypical population of CD1d-α-galactosylceramide (α-GalCer)-reactive human NKT cells that differ markedly from the prototypical TRAV10-TRAJ18-TRBV25-1(+) type I NKT cell repertoire. These cells express a range of TCR α- and β-chains that show differential recognition of glycolipid antigens. Two atypical NKT TCRs (TRAV21-TRAJ8-TRBV7-8 and TRAV12-3-TRAJ27-TRBV6-5) bind orthogonally over the A'-pocket of CD1d, adopting distinct docking modes that contrast with the docking mode of all type I NKT TCR-CD1d-antigen complexes. Moreover, the interactions with α-GalCer differ between the type I and these atypical NKT TCRs. Accordingly, diverse NKT TCR repertoire usage manifests in varied docking strategies and specificities towards CD1d-α-GalCer and related antigens, thus providing far greater scope for diverse glycolipid antigen recognition.


  • Organizational Affiliation
    • Infection and Immunity Program &Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.

Macromolecule Content 

  • Total Structure Weight: 95.29 kDa 
  • Atom Count: 6,540 
  • Modeled Residue Count: 817 
  • Deposited Residue Count: 833 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TCR Alpha Chain-TRAV21-TRAJ8207Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0B4J279 (Homo sapiens)
Explore A0A0B4J279 
Go to UniProtKB:  A0A0B4J279
PHAROS:  A0A0B4J279
GTEx:  ENSG00000211801 
Find proteins for P01848 (Homo sapiens)
Explore P01848 
Go to UniProtKB:  P01848
PHAROS:  P01848
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP01848A0A0B4J279
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TCR Beta Chain-TRBV7-8243Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for A0A5B9 (Homo sapiens)
Explore A0A5B9 
Go to UniProtKB:  A0A5B9
PHAROS:  A0A5B9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5B9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1d284Homo 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
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P15813-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulinD [auth F]99Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JLS

Query on JLS



Download:Ideal Coordinates CCD File
G [auth C](15Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]tetracos-15-enamide
C48 H93 N O9
QMLKBWVXCMTWOZ-WWHSRKRPSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
E [auth C],
F [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free:  0.244 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.196 (Depositor) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.99α = 90
b = 46.3β = 122.28
c = 124.65γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Advisory, Data collection, Database references, Derived calculations
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-09-27
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-11-20
    Changes: Structure summary