4WWK | pdb_00004wwk

Crystal structure of human TCR Alpha Chain-TRAV12-3, Beta Chain-TRBV6-5, Antigen-presenting molecule CD1d, and Beta-2-microglobulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.256 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4WWK

Ligand Structure Quality Assessment 


This is version 1.7 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: 96.99 kDa 
  • Atom Count: 5,883 
  • Modeled Residue Count: 797 
  • Deposited Residue Count: 849 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TCR Alpha Chain-TRAV12-3209Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0B4J271 (Homo sapiens)
Explore A0A0B4J271 
Go to UniProtKB:  A0A0B4J271
PHAROS:  A0A0B4J271
GTEx:  ENSG00000211794 
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 GroupsA0A0B4J271P01848
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TCR Beta Chain-TRBV6-5243Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0K0K1A5 (Homo sapiens)
Explore A0A0K0K1A5 
Go to UniProtKB:  A0A0K0K1A5
PHAROS:  A0A0K0K1A5
GTEx:  ENSG00000211721 
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 GroupsA0A5B9A0A0K0K1A5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1d278Homo 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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin119Homo 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
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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: 3.10 Å
  • R-Value Free:  0.256 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.38α = 90
b = 76.07β = 90
c = 255.72γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.2: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.6: 2024-03-13
    Changes: Source and taxonomy
  • Version 1.7: 2024-10-09
    Changes: Structure summary