Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44463.82 
• Atom Count: 3155 
• Residue Count: 380 
• Unique protein chains: 2

5C9J

Human CD1c with ligands in A' and F' channel

• DOI: 10.2210/pdb5C9J/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2015-06-27 Released: 2016-03-02 
• Deposition Author(s): Tews, I., Machelett, M.M., Mansour, S., Gadola, S.D.
• Funding Organization(s): HEFCE 

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Experimental Data Snapshot

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

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

• PubMed: 26884207 
• 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 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.

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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; [e-mail] [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
T-cell surface glycoprotein CD1c,T-cell surface glycoprotein CD1b	A	281	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Beta-2-microglobulin	B	99	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
STE	A	STEARIC ACID C18 H36 O2 QIQXTHQIDYTFRH-UHFFFAOYSA-N
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DAO	A	LAURIC ACID C12 H24 O2 POULHZVOKOAJMA-UHFFFAOYSA-N

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 = 97.130	α = 90.00
b = 97.130	β = 90.00
c = 115.080	γ = 120.00

Software Package:

Software Name	Purpose
Coot	model building
XSCALE	data scaling
PHASER	phasing
XDS	data reduction
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-06-27 
• Released Date: 2016-03-02 
• Deposition Author(s): Tews, I., Machelett, M.M., Mansour, S., Gadola, S.D.

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Funding Organization	Location	Grant Number
HEFCE	United Kingdom	--

Revision History 

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