5C9J

Human CD1c with ligands in A' and F' channel

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 

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 U S A 113: E1266-E1275

  • DOI: 10.1073/pnas.1519246113
  • Primary Citation of Related Structures:  
    5C9J

  • 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; Novartis Institutes of Biomedical Research, 4058 Basel, Switzerland sgadola@gmail.com s.mansour@soton.ac.uk.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD1c,T-cell surface glycoprotein CD1bA281Homo sapiensMutation(s): 0 
Gene Names: CD1C
Find proteins for P29016 (Homo sapiens)
Explore P29016 
Go to UniProtKB:  P29016
NIH Common Fund Data Resources
PHAROS  P29016
GTEx  ENSG00000158485
Find proteins for P29017 (Homo sapiens)
Explore P29017 
Go to UniProtKB:  P29017
NIH Common Fund Data Resources
PHAROS  P29017
GTEx  ENSG00000158481
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB99Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
GTEx  ENSG00000166710
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.13α = 90
b = 97.13β = 90
c = 115.08γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
PHASERphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

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View more in-depth experimental data

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
    Changes: Database references