Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 96.16 kDa 
• Atom Count: 6500 
• Modelled Residue Count: 839 
• Deposited Residue Count: 862 
• Unique protein chains: 1

5IU9

Crystal Structure of Zebrafish Protocadherin-19 EC1-4

• PDB DOI: 10.2210/pdb5IU9/pdb

• Classification: CELL ADHESION
• Organism(s): Danio rerio
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-17 Released: 2016-11-02 
• Deposition Author(s): Cooper, S.R., Jontes, J.D., Sotomayor, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.59 Å
• R-Value Free: 0.305 
• R-Value Work: 0.246 
• R-Value Observed: 0.249 

Literature

Structural determinants of adhesion by Protocadherin-19 and implications for its role in epilepsy.

Cooper, S.R., Jontes, J.D., Sotomayor, M.

(2016) Elife 5

• PubMed: 27787195 
• DOI: 10.7554/eLife.18529
• Primary Citation of Related Structures:  
  5CO1, 5IU9


• PubMed Abstract: 
  

Non-clustered δ-protocadherins are homophilic cell adhesion molecules essential for the development of the vertebrate nervous system, as several are closely linked to neurodevelopmental disorders. Mutations in protocadherin-19 ( PCDH19 ) result in a female-limited, infant-onset form of epilepsy (PCDH19-FE). Over 100 mutations in PCDH19 have been identified in patients with PCDH19-FE, about half of which are missense mutations in the adhesive extracellular domain. Neither the mechanism of homophilic adhesion by PCDH19, nor the biochemical effects of missense mutations are understood. Here we present a crystallographic structure of the minimal adhesive fragment of the zebrafish Pcdh19 extracellular domain. This structure reveals the adhesive interface for Pcdh19, which is broadly relevant to both non-clustered δ and clustered protocadherin subfamilies. In addition, we show that several PCDH19-FE missense mutations localize to the adhesive interface and abolish Pcdh19 adhesion in in vitro assays, thus revealing the biochemical basis of their pathogenic effects during brain development.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, The Ohio State University, Columbus, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protocadherin-19 isoform 1	A, B	431	Danio rerio	Mutation(s): 0  Gene Names: pcdh19
UniProt
Find proteins for F8W3X3 (Danio rerio) Explore F8W3X3  Go to UniProtKB:  F8W3X3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	L [auth A], V [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.59 Å
• R-Value Free: 0.305 
• R-Value Work: 0.246 
• R-Value Observed: 0.249 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.39	α = 90
b = 59.776	β = 94.39
c = 165.925	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-03-17 
• Released Date: 2016-11-02 
Deposition Author(s): Cooper, S.R., Jontes, J.D., Sotomayor, M.

Revision History  

• Version 1.0: 2016-11-02
  Type: Initial release
  
• Version 1.1: 2018-03-07
  Changes: Data collection, Derived calculations
• Version 1.2: 2018-03-21
  Changes: Source and taxonomy
• Version 1.3: 2018-08-01
  Changes: Data collection, Database references