9HMA | pdb_00009hma

Cryo-EM structure of apo human separase

PDB DOI: https://doi.org/10.2210/pdb9HMA/pdb
EM Map EMD-52290: EMDB EMDataResource

Classification: CELL CYCLE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2024-12-07 Released: 2025-09-03
Deposition Author(s): Yu, J., Schmidt, S., Botto, M., Boland, A.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

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

Structural insights into cohesin cleavage by human separase

Yu, J., Schmidt, S., Botto, M., Ghent, C.M., Morgan, D.O., Boland, A.

To be published.

Macromolecule Content

Total Structure Weight: 243.22 kDa
Atom Count: 10,333
Modeled Residue Count: 1,400
Deposited Residue Count: 2,217
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Separin	A	2,217	Homo sapiens	Mutation(s): 0 Gene Names: ESPL1, ESP1, KIAA0165 EC: 3.4.22.49
UniProt & NIH Common Fund Data Resources
Find proteins for Q14674 (Homo sapiens) Explore Q14674 Go to UniProtKB: Q14674
PHAROS: Q14674 GTEx: ENSG00000135476
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q14674
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
MODEL REFINEMENT	Coot	0.9.8.92
RECONSTRUCTION	cryoSPARC	4.4.0

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030_185235
Swiss National Science Foundation	Switzerland	TMSGI3_211581

Revision History (Full details and data files)

Version 1.0: 2025-09-03
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.