5CO1

Crystal Structure of Zebrafish Protocadherin-19 EC3-4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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) ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protocadherin-19 isoform 1A, B, C, D219Danio rerioMutation(s): 0 
Gene Names: pcdh19
UniProt
Find proteins for F8W3X3 (Danio rerio)
Explore F8W3X3 
Go to UniProtKB:  F8W3X3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF8W3X3
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.355α = 90
b = 86.631β = 122.13
c = 132.583γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2018-10-31
    Changes: Data collection, Source and taxonomy