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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 / homology: / Phi812 tail tube protein / Capsid 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: EMBO J / Year: 2026
Title: Conformational changes of the baseplate regulating tail contraction of Staphylococcus phage 812.
Authors: Ján Bíňovský / Marta Šiborová / Maryna Zlatohurska / Jiří Nováček / Pavol Bárdy / Roman Baška / Karel Škubník / Tibor Botka / Martin Benešík / Roman Pantůček / Konstantinos ...Authors: Ján Bíňovský / Marta Šiborová / Maryna Zlatohurska / Jiří Nováček / Pavol Bárdy / Roman Baška / Karel Škubník / Tibor Botka / Martin Benešík / Roman Pantůček / Konstantinos Tripsianes / Pavel Plevka /
Abstract: Phages with contractile tails employ elaborate mechanisms to penetrate bacterial cell walls and deliver their genomes into the host cytoplasm. Here, we used cryo-EM to show that the baseplate of ...Phages with contractile tails employ elaborate mechanisms to penetrate bacterial cell walls and deliver their genomes into the host cytoplasm. Here, we used cryo-EM to show that the baseplate of phage 812, a member of the Kayvirus genus, which infects Gram-positive Staphylococcus strains, is formed of a core, wedge modules, and baseplate arms carrying receptor-binding proteins 1 and 2 and tripod complexes. Upon binding to a host cell, the receptor-binding proteins of phage 812 baseplate reorient and undergo conformational changes. The changes to the tripod complexes trigger the release of the central spike and weld proteins, which expose peptidoglycan-degrading domains of the hub proteins. Changes in the positions of baseplate arms are transmitted through wedge modules to tail sheath initiator proteins. The ring of the tail sheath initiator proteins expands and triggers the contraction of the tail sheath, which shortens to 50% and pushes the tail tube 10-30 nm into the bacterial cytoplasm. Homologous molecular mechanisms are probably shared by phages of the Herelleviridae family with contractile tails to infect Gram-positive bacteria.
History
DepositionApr 15, 2024Deposition site: PDBE / Processing site: PDBE
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
8PHENIXmodel refinement
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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