3HE6 | pdb_00003he6

Crystal structure of mouse CD1d-alpha-galactosylceramide with mouse Valpha14-Vbeta8.2 NKT TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.298 (Depositor), 0.310 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.265 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Differential recognition of CD1d-alpha-galactosyl ceramide by the V beta 8.2 and V beta 7 semi-invariant NKT T cell receptors

Pellicci, D.G.Patel, O.Kjer-Nielsen, L.Pang, S.S.Sullivan, L.C.Kyparissoudis, K.Brooks, A.G.Reid, H.H.Gras, S.Lucet, I.S.Koh, R.Smyth, M.J.Mallevaey, T.Matsuda, J.L.Gapin, L.McCluskey, J.Godfrey, D.I.Rossjohn, J.

(2009) Immunity 31: 47-59

  • DOI: https://doi.org/10.1016/j.immuni.2009.04.018
  • Primary Citation Related Structures: 
    3HE6, 3HE7, 3HUJ

  • PubMed Abstract: 

    The semi-invariant natural killer T cell receptor (NKT TCR) recognizes CD1d-lipid antigens. Although the TCR alpha chain is typically invariant, the beta chain expression is more diverse, where three V beta chains are commonly expressed in mice. We report the structures of V alpha 14-V beta 8.2 and V alpha 14-V beta 7 NKT TCRs in complex with CD1d-alpha-galactosylceramide (alpha-GalCer) and the 2.5 A structure of the human NKT TCR-CD1d-alpha-GalCer complex. Both V beta 8.2 and V beta 7 NKT TCRs and the human NKT TCR ligated CD1d-alpha-GalCer in a similar manner, highlighting the evolutionarily conserved interaction. However, differences within the V beta domains of the V beta 8.2 and V beta 7 NKT TCR-CD1d complexes resulted in altered TCR beta-CD1d-mediated contacts and modulated recognition mediated by the invariant alpha chain. Mutagenesis studies revealed the differing contributions of V beta 8.2 and V beta 7 residues within the CDR2 beta loop in mediating contacts with CD1d. Collectively we provide a structural basis for the differential NKT TCR V beta usage in NKT cells.


  • Organizational Affiliation
    • Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia.

Macromolecule Content 

  • Total Structure Weight: 97.99 kDa 
  • Atom Count: 6,703 
  • Modeled Residue Count: 824 
  • Deposited Residue Count: 852 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1d1302Mus musculusMutation(s): 0 
Gene Names: Cd1d1Cd1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11609 (Mus musculus)
Explore P11609 
Go to UniProtKB:  P11609
IMPC:  MGI:107674
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11609
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P11609-1
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Mus musculusMutation(s): 0 
Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
IMPC:  MGI:88127
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01887
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Valpha14(mouse variable domain, human constant domain)207Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Vbeta8.2(mouse variable domain, human constant domain)244Mus musculusMutation(s): 0 
UniProt
Find proteins for P01850 (Homo sapiens)
Explore P01850 
Go to UniProtKB:  P01850
Entity Groups
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UniProt GroupP01850
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGH

Query on AGH



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.298 (Depositor), 0.310 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.265 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.113α = 90
b = 81.506β = 90
c = 233.451γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2020-01-29
    Changes: Advisory, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-30
    Changes: Structure summary