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- EMDB-55977: Phage 812 baseplate in the pre-contraction state - composite -

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Basic information

Entry
Database: EMDB / ID: EMD-55977
TitlePhage 812 baseplate in the pre-contraction state - composite
Map dataPhage 812 baseplate in the pre-contraction state; composite map
Sample
  • Virus: Staphylococcus phage 812K1/420 (virus)
Keywordsphage / baseplate / VIRUS
Biological speciesStaphylococcus phage 812K1/420 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsBinovsky J / Plevka P
Funding supportEuropean Union, Czech Republic, 2 items
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
DepositionDec 5, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55977.png

Downloads & links

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Map

FileDownload / File: emd_55977.map.gz / Format: CCP4 / Size: 193.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhage 812 baseplate in the pre-contraction state; composite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 267 pix.
= 445.142 Å		1.67 Å/pix.
x 441 pix.
= 735.235 Å		1.67 Å/pix.
x 430 pix.
= 716.896 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.6672 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum0.0 - 7.791647
Average (Standard dev.)0.078016914 (±0.26353857)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin107105183
Dimensions441430267
Spacing430441267
CellA: 716.896 Å / B: 735.23517 Å / C: 445.1424 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Staphylococcus phage 812K1/420

EntireName: Staphylococcus phage 812K1/420 (virus)
Components
  • Virus: Staphylococcus phage 812K1/420 (virus)

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Supramolecule #1: Staphylococcus phage 812K1/420

SupramoleculeName: Staphylococcus phage 812K1/420 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#26
Details: Propagated in S. aureus SA 812 (CCM 4028) planktonic culture and purified on a CsCl gradient.
NCBI-ID: 3434241 / Sci species name: Staphylococcus phage 812K1/420 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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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

BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTristris
10.0 mMNaClsodium chloride
10.0 mMCaCl2calcium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
Details10e9 PFU/ml

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 26731 / Average exposure time: 2.0 sec. / Average electron dose: 40.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 22031
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)

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