9ZN0 | pdb_00009zn0

Crystal structure of the Commd10 S50E HN domain mutant in domain swapped conformation

PDB DOI: https://doi.org/10.2210/pdb9ZN0/pdb

Classification: EXOCYTOSIS
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-12-11 Released: 2026-01-21
Deposition Author(s): Collins, B.M., Healy, M.D., Liu, M., Hall, R.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.243 (Depositor), 0.243 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

A remarkable case of conserved domain swapping in the COMMD family of proteins

Collins, B.M., Healy, M.D., Liu, M., Hall, R.

To be published.

Macromolecule Content

Total Structure Weight: 55.6 kDa
Atom Count: 3,860
Modeled Residue Count: 462
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COMM domain-containing protein 10	A, B, C, D	121	Homo sapiens	Mutation(s): 1 Gene Names: COMMD10, HSPC305, PTD002
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6G5 (Homo sapiens) Explore Q9Y6G5 Go to UniProtKB: Q9Y6G5
PHAROS: Q9Y6G5 GTEx: ENSG00000145781
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y6G5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LEA Query on LEA Download Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain F [auth D] MOL2 format, chain E [auth C] MOL2 format, chain F [auth D] mmCIF format, chain E [auth C] mmCIF format, chain F [auth D]	E [auth C], F [auth D]	PENTANOIC ACID C₅ H₁₀ O₂ NQPDZGIKBAWPEJ-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain F [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.243 (Depositor), 0.243 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.759	α = 90
b = 92.173	β = 111.339
c = 59.815	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-01-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History (Full details and data files)

Version 1.0: 2026-01-21
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.