9SF9 | pdb_00009sf9

Dimeric form of the Streptococcus pyogenes nuclease A (SpnA)

• PDB DOI: https://doi.org/10.2210/pdb9SF9/pdb
• EM Map EMD-54817: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Streptococcus pyogenes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-08-19 Released: 2026-09-02 
• Deposition Author(s): Bennig, I.A., Strobaek, J., Marmede, R., Sellerberg, A., Neumann, A., Friaes, A., Ramirez, M., Hall, M., Collin, M., Malmstrom, L., Ekstrom, S., Frick, I., Bjorck, L., Happonen, L.J.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Dimeric Streptococcus pyogenes nuclease A SpnA

Bennig, I.A., Strobaek, J., Marmede, R., Neumann, A., Friaes, A., Ramirez, M., Hall, M., Collin, M., Malmstrom, L., Ekstrom, S., Frick, I., Bjorck, L., Happonen, H.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 124.18 kDa 
• Atom Count: 7,560 
• Modeled Residue Count: 1,075 
• Deposited Residue Count: 1,126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease/exonuclease/phosphatase domain-containing protein	A, B	563	Streptococcus pyogenes	Mutation(s): 0  Gene Names: SPy_0747
UniProt
Find proteins for Q9A0J7 (Streptococcus pyogenes serotype M1) Explore Q9A0J7  Go to UniProtKB:  Q9A0J7

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-02 
Deposition Author(s): Bennig, I.A., Strobaek, J., Marmede, R., Sellerberg, A., Neumann, A., Friaes, A., Ramirez, M., Hall, M., Collin, M., Malmstrom, L., Ekstrom, S., Frick, I., Bjorck, L., Happonen, L.J.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2022-03860

Revision History  

• Version 1.0: 2026-09-02
  Type: Initial release