8TON | pdb_00008ton

Crystal Structure of Engineered Mouse Protocadherin-15 EC3-EC7 Connection

• PDB DOI: https://doi.org/10.2210/pdb8TON/pdb

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


• Deposited: 2023-08-03 Released: 2024-08-14 
• Deposition Author(s): De-la-Torre, P., Brower, J., Indzhykulian, A.
• Funding Organization(s): National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.223 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.194 (DCC) 

Starting Models: experimental

Literature

Crystal Structure of Engineered Mouse Protocadherin-15 EC3-EC7 Connection

De-la-Torre, P., Brower, J., Indzhykulian, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 28.1 kDa 
• Atom Count: 1,909 
• Modeled Residue Count: 224 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protocadherin-15 EC3-EC7	A	248	Mus musculus	Mutation(s): 0  Gene Names: Pcdh15
UniProt & NIH Common Fund Data Resources
Find proteins for Q99PJ1 (Mus musculus) Explore Q99PJ1  Go to UniProtKB:  Q99PJ1
IMPC:  MGI:1891428

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K (Subject of Investigation/LOI)	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.223 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.194 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.603	α = 90
b = 84.603	β = 90
c = 76.895	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-14 
Deposition Author(s): De-la-Torre, P., Brower, J., Indzhykulian, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)	United States	R01 DC020190
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)	United States	R01 DC017166

Revision History  

• Version 1.0: 2024-08-14
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary
• Version 1.2: 2026-02-11
  Changes: Data collection