6CUH | pdb_00006cuh

Crystal structure of the unliganded BC8B TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.232 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6CUH

This is version 1.2 of the entry. See complete history

Literature

A T-cell receptor escape channel allows broad T-cell response to CD1b and membrane phospholipids.

Shahine, A.Reinink, P.Reijneveld, J.F.Gras, S.Holzheimer, M.Cheng, T.Y.Minnaard, A.J.Altman, J.D.Lenz, S.Prandi, J.Kubler-Kielb, J.Moody, D.B.Rossjohn, J.Van Rhijn, I.

(2019) Nat Commun 10: 56-56

  • DOI: https://doi.org/10.1038/s41467-018-07898-0
  • Primary Citation Related Structures: 
    6CUG, 6CUH, 6D64

  • PubMed Abstract: 

    CD1 proteins are expressed on dendritic cells, where they display lipid antigens to T-cell receptors (TCRs). Here we describe T-cell autoreactivity towards ubiquitous human membrane phospholipids presented by CD1b. These T-cells discriminate between two major types of lipids, sphingolipids and phospholipids, but were broadly cross-reactive towards diverse phospholipids including phosphatidylcholine, phosphatidylinositol and phosphatidylethanolamine. The crystal structure of a representative TCR bound to CD1b-phosphatidylcholine provides a molecular mechanism for this promiscuous recognition. We observe a lateral escape channel in the TCR, which shunted phospholipid head groups sideways along the CD1b-TCR interface, without contacting the TCR. Instead the TCR recognition site involved the neck region phosphate that is common to all major self-phospholipids but absent in sphingolipids. Whereas prior studies have focused on foreign lipids or rare self-lipids, we define a new molecular mechanism of promiscuous recognition of common self-phospholipids including those that are known targets in human autoimmune disease.


  • Organizational Affiliation
    • Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.

Macromolecule Content 

  • Total Structure Weight: 50.65 kDa 
  • Atom Count: 3,482 
  • Modeled Residue Count: 427 
  • Deposited Residue Count: 452 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
T-cell Receptor alpha variable, TRAV 9-2. BC8B TCR207Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
T-cell Receptor beta variable, TRBV 6-2. BC8B TCR245Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.232 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.616α = 90
b = 76.876β = 90
c = 119.95γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary