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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: To Be Published
Title: Dimeric Streptococcus pyogenes nuclease A SpnA
Authors: 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.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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