4X6F | pdb_00004x6f

CD1a binary complex with sphingomyelin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.224 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 45.35 kDa 
  • Atom Count: 3,175 
  • Modeled Residue Count: 361 
  • Deposited Residue Count: 386 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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:|  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
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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 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
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

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Ligand Structure Quality Assessment 


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