Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.61 kDa 
• Atom Count: 2,043 
• Modelled Residue Count: 218 
• Deposited Residue Count: 583 
• Unique protein chains: 1

 5A2F

Two membrane distal IgSF domains of CD166

• PDB DOI:  https://doi.org/10.2210/pdb5A2F/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2015-05-18 Released: 2015-07-22 
• Deposition Author(s): Chappell, P.E., Johnson, S., Lea, S.M., Brown, M.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.239 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 

Literature

Structures of Cd6 and its Ligand Cd166 Give Insight Into Their Interaction.

Chappell, P.E., Garner, L.I., Yan, J., Metcalfe, C., Hatherley, D., Johnson, S., Robinson, C.V., Lea, S.M., Brown, M.H.

(2015) Structure 23: 1426

• PubMed: 26146185 
• DOI: https://doi.org/10.1016/j.str.2015.05.019
• Primary Citation of Related Structures:  
  5A2E, 5A2F


• PubMed Abstract: 
  

CD6 is a transmembrane protein with an extracellular region containing three scavenger receptor cysteine rich (SRCR) domains. The membrane proximal domain of CD6 binds the N-terminal immunoglobulin superfamily (IgSF) domain of another cell surface receptor, CD166, which also engages in homophilic interactions. CD6 expression is mainly restricted to T cells, and the interaction between CD6 and CD166 regulates T-cell activation. We have solved the X-ray crystal structures of the three SRCR domains of CD6 and two N-terminal domains of CD166. This first structure of consecutive SRCR domains reveals a nonlinear organization. We characterized the binding sites on CD6 and CD166 and showed that a SNP in CD6 causes glycosylation that hinders the CD6/CD166 interaction. Native mass spectrometry analysis showed that there is competition between the heterophilic and homophilic interactions. These data give insight into how interactions of consecutive SRCR domains are perturbed by SNPs and potential therapeutic reagents.

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Organizational Affiliation: 

Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CD166 ANTIGEN	A	583	Homo sapiens	Mutation(s): 0  Gene Names: ALCAM, MEMD
UniProt & NIH Common Fund Data Resources
Find proteins for Q13740 (Homo sapiens) Explore Q13740  Go to UniProtKB:  Q13740
PHAROS:  Q13740

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.239 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.32	α = 90
b = 72.32	β = 90
c = 105.04	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-22 
Deposition Author(s): Chappell, P.E., Johnson, S., Lea, S.M., Brown, M.H.

Revision History  

• Version 1.0: 2015-07-22
  Type: Initial release
  
• Version 1.1: 2015-08-19
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary