5ERP | pdb_00005erp

Crystal structure of human Desmocollin-2 ectodomain fragment EC2-5

• PDB DOI: https://doi.org/10.2210/pdb5ERP/pdb

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


• Deposited: 2015-11-14 Released: 2016-06-15 
• Deposition Author(s): Harrison, O.J., Brasch, J., Shapiro, L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.262 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

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 U S A 113: 7160-7165

• PubMed: 27298358 
• DOI: https://doi.org/10.1073/pnas.1606272113
• Primary Citation Related Structures: 
  5EQX, 5ERD, 5ERP, 5IRY, 5J5J


• 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 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.

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Organizational Affiliation: 
• Department of Systems Biology, Columbia University, New York, NY 10032; Howard Hughes Medical Institute, Columbia University, New York, NY 10032;
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032;
Department of Systems Biology, Columbia University, New York, NY 10032; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032;
Department of Systems Biology, Columbia University, New York, NY 10032; Howard Hughes Medical Institute, Columbia University, New York, NY 10032; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032; Department of Medicine, Columbia University, New York, NY 10032; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10032 [e-mail] [e-mail].
Department of Systems Biology, Columbia University, New York, NY 10032; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10032 [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 106.36 kDa 
• Atom Count: 7,296 
• Modeled Residue Count: 881 
• Deposited Residue Count: 902 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Desmocollin-2	A, B	451	Homo sapiens	Mutation(s): 0  Gene Names: DSC2, CDHF2, DSC3
UniProt & NIH Common Fund Data Resources
Find proteins for Q02487 (Homo sapiens) Explore Q02487  Go to UniProtKB:  Q02487
PHAROS:  Q02487 GTEx:  ENSG00000134755
Glycosylation
Glycosylation Sites: 7		Go to GlyGen: Q02487-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth A], K [auth A], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN	AA [auth B], BA [auth B], CA [auth B], DA [auth B], F [auth A], G [auth A], H [auth A], I [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
SO4	PA [auth B], V [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	QA [auth B], RA [auth B], W [auth A], X [auth A], Y [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.262 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.216	α = 90
b = 94.166	β = 93.66
c = 126.307	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-06-15 
Deposition Author(s): Harrison, O.J., Brasch, J., Shapiro, L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM062270

Revision History  

• Version 1.0: 2016-06-15
  Type: Initial release
  
• Version 1.1: 2016-06-29
  Changes: Database references
• Version 1.2: 2016-07-13
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 3.0: 2024-12-25
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary