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- PDB-9pha: CryoEM structure of the YonE portal protein from Bacillus phage SPbeta -

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Basic information

Entry
Database: PDB / ID: 9pha
TitleCryoEM structure of the YonE portal protein from Bacillus phage SPbeta
ComponentsSPbeta prophage-derived uncharacterized protein YonE
KeywordsVIRAL PROTEIN / Portal protein / antiphage defence
Function / homologySPbeta prophage-derived uncharacterized protein YonE
Function and homology information
Biological speciesSpbetavirus SPbeta
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMishra, B.P. / Ve, T.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT200100572 Australia
National Health and Medical Research Council (NHMRC, Australia)1196590 Australia
CitationJournal: To Be Published
Title: Molecular characterisation of the Bacillus subtilis SpbK antiphage defence system
Authors: Mishra, B.P. / Ve, T.
History
DepositionJul 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPbeta prophage-derived uncharacterized protein YonE
B: SPbeta prophage-derived uncharacterized protein YonE
C: SPbeta prophage-derived uncharacterized protein YonE
D: SPbeta prophage-derived uncharacterized protein YonE
E: SPbeta prophage-derived uncharacterized protein YonE
F: SPbeta prophage-derived uncharacterized protein YonE
G: SPbeta prophage-derived uncharacterized protein YonE
H: SPbeta prophage-derived uncharacterized protein YonE
I: SPbeta prophage-derived uncharacterized protein YonE
J: SPbeta prophage-derived uncharacterized protein YonE
K: SPbeta prophage-derived uncharacterized protein YonE
L: SPbeta prophage-derived uncharacterized protein YonE


Theoretical massNumber of molelcules
Total (without water)666,34112
Polymers666,34112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
SPbeta prophage-derived uncharacterized protein YonE


Mass: 55528.391 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spbetavirus SPbeta / Gene: yonE, BSU21120 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O31953
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: YonE portal protein from SPbeta phage / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Spbetavirus SPbeta
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22320 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00230828
ELECTRON MICROSCOPYf_angle_d0.49241592
ELECTRON MICROSCOPYf_dihedral_angle_d4.6313924
ELECTRON MICROSCOPYf_chiral_restr0.0354464
ELECTRON MICROSCOPYf_plane_restr0.0035280

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