5C9J

Human CD1c with ligands in A' and F' channel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cholesteryl esters stabilize human CD1c conformations for recognition by self-reactive T cells.

Mansour, S.Tocheva, A.S.Cave-Ayland, C.Machelett, M.M.Sander, B.Lissin, N.M.Molloy, P.E.Baird, M.S.Stubs, G.Schroder, N.W.Schumann, R.R.Rademann, J.Postle, A.D.Jakobsen, B.K.Marshall, B.G.Gosain, R.Elkington, P.T.Elliott, T.Skylaris, C.K.Essex, J.W.Tews, I.Gadola, S.D.

(2016) Proc.Natl.Acad.Sci.USA 113: E1266-E1275

  • DOI: 10.1073/pnas.1519246113

  • PubMed Abstract: 
  • Cluster of differentiation 1c (CD1c)-dependent self-reactive T cells are abundant in human blood, but self-antigens presented by CD1c to the T-cell receptors of these cells are poorly understood. Here we present a crystal structure of CD1c determined ...

    Cluster of differentiation 1c (CD1c)-dependent self-reactive T cells are abundant in human blood, but self-antigens presented by CD1c to the T-cell receptors of these cells are poorly understood. Here we present a crystal structure of CD1c determined at 2.4 Å revealing an extended ligand binding potential of the antigen groove and a substantially different conformation compared with known CD1c structures. Computational simulations exploring different occupancy states of the groove reenacted these different CD1c conformations and suggested cholesteryl esters (CE) and acylated steryl glycosides (ASG) as new ligand classes for CD1c. Confirming this, we show that binding of CE and ASG to CD1c enables the binding of human CD1c self-reactive T-cell receptors. Hence, human CD1c adopts different conformations dependent on ligand occupancy of its groove, with CE and ASG stabilizing CD1c conformations that provide a footprint for binding of CD1c self-reactive T-cell receptors.


    Organizational Affiliation

    Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, United Kingdom; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom; sgadola@gmail.com s.mansour@soton.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD1c,T-cell surface glycoprotein CD1b
A
281Homo sapiensMutation(s): 0 
Gene Names: CD1C, CD1B
Find proteins for P29017 (Homo sapiens)
Go to Gene View: CD1C
Go to UniProtKB:  P29017
Find proteins for P29016 (Homo sapiens)
Go to Gene View: CD1B
Go to UniProtKB:  P29016
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
99Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STE
Query on STE

Download SDF File 
Download CCD File 
A
STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DAO
Query on DAO

Download SDF File 
Download CCD File 
A
LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 97.130α = 90.00
b = 97.130β = 90.00
c = 115.080γ = 120.00
Software Package:
Software NamePurpose
Cootmodel building
XSCALEdata scaling
PHASERphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
HEFCEUnited Kingdom--

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-09
    Type: Database references