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- EMDB-54816: Monomeric form of the Streptococcus pyogenes nuclease A (SpnA) -

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Basic information

Entry
Database: EMDB / ID: EMD-54816
TitleMonomeric form of the Streptococcus pyogenes nuclease A (SpnA)
Map data
Sample
  • Complex: Streptococcus pyogenes nuclease A, SpnA
    • Complex: Streptococcus pyogenes nuclease A, SpnA
      • Protein or peptide: Endonuclease/exonuclease/phosphatase domain-containing protein
KeywordsStreptococcus pyogenes / nuclease / SpnA / DNA BINDING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsBennig IA / Strobaek J / Marmede R / Sellerberg A / Neumann A / Friaes A / Ramirez M / Hall M / Collin M / Malmstrom L ...Bennig IA / 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 LJ
Funding support Sweden, 1 items
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, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54816.png

Downloads & links

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Map

FileDownload / File: emd_54816.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 200 pix.
= 228. Å		1.14 Å/pix.
x 200 pix.
= 228. Å		1.14 Å/pix.
x 200 pix.
= 228. Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.5725616 - 2.526458
Average (Standard dev.)-0.00051773817 (±0.0516695)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 228.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54816_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54816_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Streptococcus pyogenes nuclease A, SpnA

EntireName: Streptococcus pyogenes nuclease A, SpnA
Components
  • Complex: Streptococcus pyogenes nuclease A, SpnA
    • Complex: Streptococcus pyogenes nuclease A, SpnA
      • Protein or peptide: Endonuclease/exonuclease/phosphatase domain-containing protein

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Supramolecule #1: Streptococcus pyogenes nuclease A, SpnA

SupramoleculeName: Streptococcus pyogenes nuclease A, SpnA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptococcus pyogenes (bacteria)

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Supramolecule #2: Streptococcus pyogenes nuclease A, SpnA

SupramoleculeName: Streptococcus pyogenes nuclease A, SpnA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all

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

MacromoleculeName: Endonuclease/exonuclease/phosphatase domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Molecular weightTheoretical: 61.96652 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: IVKIGEIQGA SHTSPLLKKA VTVEQVVVTY LDDSTHFYVQ DLNGDGDLAT SDGIRVFAKN AKVQVGDVLT ISGEVEEFFG RGYEERKQT DLTITQIVAK AVTKTGTAQV PSPLVLGKDR IAPANIIDND GLRVFDPEED AIDYWESMEG MLVAVDDAKI L GPMKNKEI ...String:
IVKIGEIQGA SHTSPLLKKA VTVEQVVVTY LDDSTHFYVQ DLNGDGDLAT SDGIRVFAKN AKVQVGDVLT ISGEVEEFFG RGYEERKQT DLTITQIVAK AVTKTGTAQV PSPLVLGKDR IAPANIIDND GLRVFDPEED AIDYWESMEG MLVAVDDAKI L GPMKNKEI YVLPGSSTRP LNNSGGVLLP ANSYNTDVIP VLFKKGKQII KAGDSYKGRL AGPVSYSYGN YKVFVDDSKN MP SLMDGHL KPEKTNLQKD LSKLSIASYN IENFSANPSS TKDEKVKRIA ESFIHDLNAP DIIGLIEVQD NNGPTDDGTT DAT QSAQRL IDAIKKLGGP TYRYVDIAPE NNVDGGQPGG NIRTGFLYQP ERVSLSDKPK GGARDALTWV NGELNLSVGR IDPT NAAWK DVRKSLAAEF IFQGRKVVVV ANHLNSKRGD NALYGCVQPV TFKSEQRRHV LANMLAQFAK EGAKHQANIV MLGDF NDFE FTKTIQLIEE GDMVNLVSRH DISDRYSYFH QGNNQTLDNI LVSRHLLDHY EFDMVHVNSP FMEAHGRASD HDPLLL QL

UniProtKB: Endonuclease/exonuclease/phosphatase domain-containing protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 134130
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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