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- PDB-9f06: Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 t... -

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Basic information

Entry
Database: PDB / ID: 9f06
TitleCryo-EM structure of Staphylococcus aureus bacteriophage phi812 tail in the post-contraction state - tube proteins
ComponentsCapsid protein
KeywordsVIRUS / bacteriophage / phage / contractile / phi812 / tail
Function / homologyCapsid protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBinovsky, J. / Siborova, M. / Plevka, P.
Funding supportEuropean Union, Czech Republic, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101043452European Union
Other governmentLX22NP05103 Czech Republic
CitationJournal: To Be Published
Title: Cell attachment and tail contraction of S. aureus phage phi812
Authors: Binovsky, J. / Siborova, M. / Plevka, P.
History
DepositionApr 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 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: Capsid protein
B: Capsid protein
C: Capsid protein


Theoretical massNumber of molelcules
Total (without water)47,8293
Polymers47,8293
Non-polymers00
Water00
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 11
A: Capsid protein
B: Capsid protein
C: Capsid protein

A: Capsid protein
B: Capsid protein
C: Capsid protein

A: Capsid protein
B: Capsid protein
C: Capsid protein

A: Capsid protein
B: Capsid protein
C: Capsid protein

A: Capsid protein
B: Capsid protein
C: Capsid protein


Theoretical massNumber of molelcules
Total (without water)765,26348
Polymers765,26348
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation15
MethodUCSF CHIMERA

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Components

#1: Protein Capsid protein / tail tube protein


Mass: 15942.970 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / References: UniProt: A1YTP2
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

Component
IDNameTypeEntity IDParent-IDSource
1Staphylococcus phage 812VIRUSall0NATURAL
2TailCOMPLEXall1NATURAL
3Tail tubeCOMPLEXall2NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Staphylococcus phage 812 (virus)307898
32Staphylococcus phage 812 (virus)307898
43Staphylococcus phage 812 (virus)307898
Details of virus
IDEntity assembly-IDEmptyEnvelopedIsolateType
11YESNOSPECIESVIRION
22
33
Buffer solutionpH: 8 / Details: 50mM Tris, 10mM NaCl, 10mM CaCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingAverage exposure time: 7 sec. / Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 15371
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
10RELION4initial Euler assignment
11RELION4final Euler assignment
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12906 / Symmetry type: POINT

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