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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1038/ni.3098
  • Primary Citation of Related Structures:  

  • 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 proto ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD1a
A
281Homo sapiensMutation(s): 0 
Gene Names: CD1A
Find proteins for P06126 (Homo sapiens)
Go to Gene View: CD1A
Go to UniProtKB:  P06126
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
105Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3XU
Query on 3XU

Download SDF File 
Download CCD File 
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
N_nervonoyl_D_erythro_sphingosylphosphorylcholine
C47 H94 N2 O6 P
WKZHECFHXLTOLJ-SSBLBVCXSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.380α = 90.00
b = 90.210β = 90.00
c = 107.790γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-02-18
    Type: Database references
  • Version 1.2: 2015-02-25
    Type: Database references
  • Version 1.3: 2015-03-04
    Type: Structure summary