4ZI9

Structure of mouse clustered PcdhgA1 EC1-3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity.

Nicoludis, J.M.Lau, S.Y.Scharfe, C.P.Marks, D.S.Weihofen, W.A.Gaudet, R.

(2015) Structure 23: 2087-2098

  • DOI: 10.1016/j.str.2015.09.005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Clustered protocadherin (Pcdh) proteins mediate dendritic self-avoidance in neurons via specific homophilic interactions in their extracellular cadherin (EC) domains. We determined crystal structures of EC1-EC3, containing the homophilic specificity- ...

    Clustered protocadherin (Pcdh) proteins mediate dendritic self-avoidance in neurons via specific homophilic interactions in their extracellular cadherin (EC) domains. We determined crystal structures of EC1-EC3, containing the homophilic specificity-determining region, of two mouse clustered Pcdh isoforms (PcdhγA1 and PcdhγC3) to investigate the nature of the homophilic interaction. Within the crystal lattices, we observe antiparallel interfaces consistent with a role in trans cell-cell contact. Antiparallel dimerization is supported by evolutionary correlations. Two interfaces, located primarily on EC2-EC3, involve distinctive clustered Pcdh structure and sequence motifs, lack predicted glycosylation sites, and contain residues highly conserved in orthologs but not paralogs, pointing toward their biological significance as homophilic interaction interfaces. These two interfaces are similar yet distinct, reflecting a possible difference in interaction architecture between clustered Pcdh subfamilies. These structures initiate a molecular understanding of clustered Pcdh assemblies that are required to produce functional neuronal networks.


    Organizational Affiliation

    Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA. Electronic address: wilhelm.weihofen@novartis.com.,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.,Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen 72076, Germany.,Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA. Electronic address: gaudet@mcb.harvard.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MCG133388, isoform CRA_t
A, B
318Mus musculusMutation(s): 0 
Gene Names: Pcdhga1
Find proteins for Q91XZ0 (Mus musculus)
Go to UniProtKB:  Q91XZ0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 67.751α = 90.00
b = 63.687β = 99.69
c = 107.486γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PHASERphasing
HKL-2000data reduction

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 Sciences (NIH/NIGMS)United StatesP41 GM103403
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10 RR029205
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History 

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2015-11-04
    Type: Database references
  • Version 1.2: 2015-11-18
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-12-04
    Type: Author supporting evidence