Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 75.57 kDa 
• Atom Count: 5,655 
• Modelled Residue Count: 636 
• Deposited Residue Count: 668 
• Unique protein chains: 1

 4ZI8

Structure of mouse clustered PcdhgC3 EC1-3

• PDB DOI: 10.2210/pdb4ZI8/pdb

• Classification: CELL ADHESION
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-04-27 Released: 2015-10-28 
• Deposition Author(s): Nicoludis, J.M., Lau, S.-Y., Scharfe, C.P.I., Marks, D.S., Weihofen, W.A., Gaudet, R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Research Resources (NIH/NCRR), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.239 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 

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

• PubMed: 26481813 
• DOI: 10.1016/j.str.2015.09.005
• Primary Citation of Related Structures:  
  4ZI8, 4ZI9


• 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-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.

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Organizational Affiliation: 

Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Pcdhgc3	A, B	334	Mus musculus	Mutation(s): 0  Gene Names: Pcdhgc3
UniProt & NIH Common Fund Data Resources
Find proteins for Q91XX1 (Mus musculus) Explore Q91XX1  Go to UniProtKB:  Q91XX1
IMPC:  MGI:1935201

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	U [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
MPD	M [auth A], V [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
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], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	T [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.239 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data DOI: 10.15785/SBGRID/174

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.123	α = 90
b = 82.286	β = 90
c = 237.69	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-10-28 
Deposition Author(s): Nicoludis, J.M., Lau, S.-Y., Scharfe, C.P.I., Marks, D.S., Weihofen, W.A., Gaudet, R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41 GM103403
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	S10 RR029205
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357

Revision History  

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