4X6F

CD1a binary complex with sphingomyelin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3XUClick on this verticalbar to view details

This is version 1.6 of the entry. See complete history


Literature

alpha beta T cell antigen receptor recognition of CD1a presenting self lipid ligands.

Birkinshaw, R.W.Pellicci, D.G.Cheng, T.Y.Keller, A.N.Sandoval-Romero, M.Gras, S.de Jong, A.Uldrich, A.P.Moody, D.B.Godfrey, D.I.Rossjohn, J.

(2015) Nat Immunol 16: 258-266

  • DOI: https://doi.org/10.1038/ni.3098
  • Primary Citation of Related Structures:  
    4X6B, 4X6C, 4X6D, 4X6E, 4X6F

  • PubMed Abstract: 

    A central paradigm in αβ T cell-mediated immunity is the simultaneous co-recognition of antigens and antigen-presenting molecules by the αβ T cell antigen receptor (TCR). CD1a presents a broad repertoire of lipid-based antigens. We found that a prototypical autoreactive TCR bound CD1a when it was presenting a series of permissive endogenous ligands, while other lipid ligands were nonpermissive to TCR binding. The structures of two TCR-CD1a-lipid complexes showed that the TCR docked over the A' roof of CD1a in a manner that precluded direct contact with permissive ligands. Nonpermissive ligands indirectly inhibited TCR binding by disrupting the TCR-CD1a contact zone. The exclusive recognition of CD1a by the TCR represents a previously unknown mechanism whereby αβ T cells indirectly sense self antigens that are bound to an antigen-presenting molecule.


  • Organizational Affiliation

    1] Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Australia. [2] ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD1a281Homo sapiensMutation(s): 2 
Gene Names: CD1A
UniProt & NIH Common Fund Data Resources
Find proteins for P06126 (Homo sapiens)
Explore P06126 
Go to UniProtKB:  P06126
PHAROS:  P06126
GTEx:  ENSG00000158477 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06126
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin105Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3XU
Query on 3XU

Download Ideal Coordinates CCD File 
C [auth A](4S,7S,23Z)-4-hydroxy-7-[(1S,2Z)-1-hydroxyhexadec-2-en-1-yl]-N,N,N-trimethyl-9-oxo-3,5-dioxa-8-aza-4-phosphadotriacont- 23-en-1-aminium 4-oxide
C47 H94 N2 O6 P
WKZHECFHXLTOLJ-SSBLBVCXSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.38α = 90
b = 90.21β = 90
c = 107.79γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3XUClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Database references
  • Version 1.2: 2015-02-25
    Changes: Database references
  • Version 1.3: 2015-03-04
    Changes: Structure summary
  • Version 1.4: 2022-12-21
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.5: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.6: 2024-10-09
    Changes: Structure summary