9HN5 | pdb_00009hn5

Cryo-EM structure of human separase bound to phosphorylated SCC1 (100-320 aa)

• PDB DOI: https://doi.org/10.2210/pdb9HN5/pdb
• EM Map EMD-52307: EMDB EMDataResource

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2024-12-10 Released: 2025-09-03 
• Deposition Author(s): Yu, J., Schmidt, S., Botto, M., Boland, A.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.96 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 263.67 kDa 
• Atom Count: 11,314 
• Modeled Residue Count: 1,518 
• Deposited Residue Count: 2,399 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Double-strand-break repair protein rad21 homolog	A [auth B]	227	Homo sapiens	Mutation(s): 0  Gene Names: RAD21, HR21, KIAA0078, NXP1, SCC1
UniProt & NIH Common Fund Data Resources
Find proteins for O60216 (Homo sapiens) Explore O60216  Go to UniProtKB:  O60216
PHAROS:  O60216 GTEx:  ENSG00000164754

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Separin	B [auth A]	2,172	Homo sapiens	Mutation(s): 1  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A [auth B]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.96 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

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Yu, J., Schmidt, S., Botto, M., Boland, A.

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

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release