4X6C

CD1a ternary complex with lysophosphatidylcholine and BK6 TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.176 

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, C
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, D
105Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
TCR alpha
E, G
207Homo sapiensMutation(s): 0 
Gene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
TCR beta
F, H
245Homo sapiensMutation(s): 0 
Gene Names: TRBC1
Find proteins for P01850 (Homo sapiens)
Go to UniProtKB:  P01850
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
42H
Query on 42H

Download SDF File 
Download CCD File 
A, C
(4R,7R,18Z)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium 4-oxide
C26 H53 N O7 P
YAMUFBLWGFFICM-PTGWMXDISA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 89.273α = 90.00
b = 142.144β = 90.00
c = 175.752γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-28
    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