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- PDB-9sf9: Dimeric form of the Streptococcus pyogenes nuclease A (SpnA) -

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Basic information

Entry
Database: PDB / ID: 9sf9
TitleDimeric form of the Streptococcus pyogenes nuclease A (SpnA)
ComponentsEndonuclease/exonuclease/phosphatase domain-containing protein
KeywordsDNA BINDING PROTEIN / Streptococcus pyogenes / nuclease / SpnA
Function / homologyEndonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / catalytic activity / Endonuclease/exonuclease/phosphatase domain-containing protein
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsBennig, I.A. / Strobaek, J. / Marmede, R. / Sellerberg, A. / Neumann, A. / Friaes, A. / Ramirez, M. / Hall, M. / Collin, M. / Malmstrom, L. ...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 support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2022-03860 Sweden
CitationJournal: Commun Biol / Year: 2026
Title: Molecular mechanism of complement interference by Streptococcus pyogenes nuclease A.
Authors: Isabella A Bennig / Joel Ströbaek / Rafael Mamede / Anton Sellerberg / Ariane Neumann / Ana Friães / Mario Ramirez / Michael Hall / Mattias Collin / Lars Malmström / Simon Ekström / Inga- ...Authors: Isabella A Bennig / Joel Ströbaek / Rafael Mamede / Anton Sellerberg / Ariane Neumann / Ana Friães / Mario Ramirez / Michael Hall / Mattias Collin / Lars Malmström / Simon Ekström / Inga-Maria Frick / Lars Björck / Lotta J Happonen /
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 ...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.
History
DepositionAug 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2026Group: Data collection / Database references / Category: citation / em_admin
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Revision 1.1Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata / EM metadata
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Revision 1.2Oct 7, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.2Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease/exonuclease/phosphatase domain-containing protein
B: Endonuclease/exonuclease/phosphatase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)124,1752
Polymers124,1752
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Endonuclease/exonuclease/phosphatase domain-containing protein


Mass: 62087.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: SPy_0747 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A0J7
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Streptococcus pyogenes nuclease A, SpnA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5207model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126766 / Symmetry type: POINT
RefinementHighest resolution: 2.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037624
ELECTRON MICROSCOPYf_angle_d0.50610384
ELECTRON MICROSCOPYf_dihedral_angle_d4.3551081
ELECTRON MICROSCOPYf_chiral_restr0.0451233
ELECTRON MICROSCOPYf_plane_restr0.0041356

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