Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.46 kDa 
• Atom Count: 3271 
• Modelled Residue Count: 380 
• Deposited Residue Count: 380 
• Unique protein chains: 2

5C9J

Human CD1c with ligands in A' and F' channel

• PDB DOI: 10.2210/pdb5C9J/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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: 2.40 Å
• R-Value Free: 0.200 
• R-Value Work: 0.155 
• R-Value Observed: 0.158 

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

• PubMed: 26884207 
• 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 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; Novartis Institutes of Biomedical Research, 4058 Basel, Switzerland [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD1c,T-cell surface glycoprotein CD1b	A	281	Homo sapiens	Mutation(s): 0  Gene Names: CD1C, CD1B
UniProt & NIH Common Fund Data Resources
Find proteins for P29016 (Homo sapiens) Explore P29016  Go to UniProtKB:  P29016
PHAROS:  P29016
Find proteins for P29017 (Homo sapiens) Explore P29017  Go to UniProtKB:  P29017
PHAROS:  P29017
UniProt Groups	P29016P29017

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STE	E [auth A]	STEARIC ACID C18 H36 O2 QIQXTHQIDYTFRH-UHFFFAOYSA-N
DAO	C [auth A], D [auth A]	LAURIC ACID C12 H24 O2 POULHZVOKOAJMA-UHFFFAOYSA-N
PO4	I [auth A], J [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	F [auth A], G [auth A], H [auth A], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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 = 97.13	α = 90
b = 97.13	β = 90
c = 115.08	γ = 120

Software Package:

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

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
  Changes: Database references