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

Molecular mechanism of complement interference by Streptococcus pyogenes nuclease A.

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

(2026) Commun Biol 9

• PubMed: 42778653 
• DOI: https://doi.org/10.1038/s42003-026-10956-9
• Primary Citation Related Structures: 
  9SF8, 9SF9


• PubMed Abstract: 
  

  Bacteria deploy virulence factors to subvert host immunity; yet the molecular details of these interactions often remain limited. Here, we reveal the structure and host interactome of the Streptococcus pyogenes nuclease A (SpnA). We characterize the structure and dynamics of SpnA using hydrogen-deuterium exchange mass spectrometry and single-particle electron cryo microscopy, yielding the first structural insights to SpnA. This allowed us to identify an additional oligonucleotide-binding domain, whose flexible structure may play an important function in nucleolytic activity. Affinity-pulldown mass spectrometry identified the complement system membrane attack complex (MAC) C5b67 components as key interactors. Cross-linking mass spectrometry combined with integrative modeling identified the binding interfaces between SpnA and C5b67. These interfaces are conserved among genetically diverse S. pyogenes strains. Interaction between SpnA and C5b67 is suggested to prevent the assembly of a functional MAC. Our findings uncover a novel function of SpnA in complement inhibition, and identifies new potential targets to prevent and treat S. pyogenes infections.

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Organizational Affiliation: 
• Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden.
Instituto de Microbiologia, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
Gulbenkian Institute for Molecular Medicine, Lisbon, Portugal.
Structural Proteomics, Science for Life Laboratory, Lund University, Lund, Sweden.
Department of Chemistry, Umeå University, Umeå, Sweden.
Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden. [e-mail].
Science for Life Laboratory, Lund University, Lund, Sweden. [e-mail].

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
  
• Version 1.1: 2026-09-30
  Changes: Data collection, Database references
• Version 1.2: 2026-10-07
  Changes: Data collection, Database references