8UMZ | pdb_00008umz

Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection

PDB DOI: https://doi.org/10.2210/pdb8UMZ/pdb

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

Deposited: 2023-10-18 Released: 2024-11-13
Deposition Author(s): De-la-Torre, P., Martinez-Perez, K., Indzhykulian, A.
Funding Organization(s): National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free:
0.274 (Depositor), 0.281 (DCC)
R-Value Work:
0.223 (Depositor), 0.230 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection

De-la-Torre, P., Martinez-Perez, K., Indzhykulian, A.

To be published.

Macromolecule Content

Total Structure Weight: 52.29 kDa
Atom Count: 3,829
Modeled Residue Count: 444
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protocadherin-15 EC4-EC7	A, B	230	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99PJ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain H [auth A]	H [auth A], N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.274 (Depositor), 0.281 (DCC)
R-Value Work: 0.223 (Depositor), 0.230 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.276	α = 90
b = 50.613	β = 94.008
c = 88.263	γ = 90

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-11-13

Deposition Author(s):

De-la-Torre, P.

Martinez-Perez, K.

Indzhykulian, A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)	United States	R01DC020190
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)	United States	R01 DC017166