7YXY | pdb_00007yxy

Cryo-EM structure of USP9X, local refinement of monomer

PDB DOI: https://doi.org/10.2210/pdb7YXY/pdb
EM Map EMD-14369: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2022-02-16 Released: 2022-03-02
Deposition Author(s): Deme, J.C., Halabelian, L., Arrowsmith, C.H., Lea, S.M., Structural Genomics Consortium (SGC)
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 7YXY

This is version 1.2 of the entry. See complete history.

Literature

Cryo-EM structure of USP9X

Halabelian, L., Deme, J.C., Lea, S.M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 293.88 kDa
Atom Count: 14,031
Modeled Residue Count: 1,739
Deposited Residue Count: 2,579
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ubiquitin carboxyl-terminal hydrolase FAF-X	A	2,579	Homo sapiens	Mutation(s): 0 Gene Names: USP9X, DFFRX, FAM, USP9 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q93008 (Homo sapiens) Explore Q93008 Go to UniProtKB: Q93008
PHAROS: Q93008 GTEx: ENSG00000124486
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93008
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-02

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2022-03-02
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Structure summary
Version 1.2: 2025-07-02
Changes: Data collection

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.