5EQX

Crystal structure of human Desmoglein-3 ectodomain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of adhesive binding by desmocollins and desmogleins.

Harrison, O.J.Brasch, J.Lasso, G.Katsamba, P.S.Ahlsen, G.Honig, B.Shapiro, L.

(2016) Proc.Natl.Acad.Sci.USA 113: 7160-7165

  • DOI: 10.1073/pnas.1606272113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Desmosomes are intercellular adhesive junctions that impart strength to vertebrate tissues. Their dense, ordered intercellular attachments are formed by desmogleins (Dsgs) and desmocollins (Dscs), but the nature of trans-cellular interactions between ...

    Desmosomes are intercellular adhesive junctions that impart strength to vertebrate tissues. Their dense, ordered intercellular attachments are formed by desmogleins (Dsgs) and desmocollins (Dscs), but the nature of trans-cellular interactions between these specialized cadherins is unclear. Here, using solution biophysics and coated-bead aggregation experiments, we demonstrate family-wise heterophilic specificity: All Dsgs form adhesive dimers with all Dscs, with affinities characteristic of each Dsg:Dsc pair. Crystal structures of ectodomains from Dsg2 and Dsg3 and from Dsc1 and Dsc2 show binding through a strand-swap mechanism similar to that of homophilic classical cadherins. However, conserved charged amino acids inhibit Dsg:Dsg and Dsc:Dsc interactions by same-charge repulsion and promote heterophilic Dsg:Dsc interactions through opposite-charge attraction. These findings show that Dsg:Dsc heterodimers represent the fundamental adhesive unit of desmosomes and provide a structural framework for understanding desmosome assembly.


    Organizational Affiliation

    Department of Systems Biology, Columbia University, New York, NY 10032; Howard Hughes Medical Institute, Columbia University, New York, NY 10032;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Desmoglein-3
A
555Homo sapiensMutation(s): 0 
Gene Names: DSG3 (CDHF6)
Find proteins for P32926 (Homo sapiens)
Go to Gene View: DSG3
Go to UniProtKB:  P32926
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.236 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 81.909α = 90.00
b = 44.862β = 102.92
c = 106.699γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM062270

Revision History 

  • Version 1.0: 2016-06-15
    Type: Initial release
  • Version 1.1: 2016-06-29
    Type: Database references
  • Version 1.2: 2016-07-13
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations