9HMV | pdb_00009hmv

Cryo-EM structure of SA2-SCC1 complex at 2.9 angstrom

• PDB DOI: https://doi.org/10.2210/pdb9HMV/pdb
• EM Map EMD-52298: EMDB EMDataResource

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


• Deposited: 2024-12-09 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: 2.90 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: 173.42 kDa 
• Atom Count: 8,234 
• Modeled Residue Count: 1,013 
• Deposited Residue Count: 1,512 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cohesin subunit SA-2	A	1,271	Homo sapiens	Mutation(s): 0  Gene Names: STAG2, SA2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N3U4 (Homo sapiens) Explore Q8N3U4  Go to UniProtKB:  Q8N3U4
PHAROS:  Q8N3U4 GTEx:  ENSG00000101972

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Double-strand-break repair protein rad21 homolog	B	241	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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

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

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