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- EMDB-55966: Phage 812 baseplate in the post-contraction state (C1) -

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Basic information

Entry
Database: EMDB / ID: EMD-55966
TitlePhage 812 baseplate in the post-contraction state (C1)
Map dataPhage 812 baseplate in the post-contraction state (C1); postprocessed map
Sample
  • Virus: Staphylococcus phage 812K1/420 (virus)
Keywordsphage / baseplate / VIRUS
Biological speciesStaphylococcus phage 812K1/420 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.6 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: To Be Published
Title: Conformational changes of baseplate regulating tail contraction of Staphylococcus phage 812
Authors: Binovsky J / Plevka P
History
DepositionDec 5, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55966.png

Downloads & links

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Map

FileDownload / File: emd_55966.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhage 812 baseplate in the post-contraction state (C1); postprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.11 Å/pix.
x 640 pix.
= 1350.4 Å		2.11 Å/pix.
x 640 pix.
= 1350.4 Å		2.11 Å/pix.
x 640 pix.
= 1350.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.041927192 - 0.12409742
Average (Standard dev.)0.0001888695 (±0.0027213213)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 1350.3999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55966_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Phage 812 baseplate in the post-contraction state (C1); half map1

Fileemd_55966_half_map_1.map
AnnotationPhage 812 baseplate in the post-contraction state (C1); half map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Phage 812 baseplate in the post-contraction state (C1); half map2

Fileemd_55966_half_map_2.map
AnnotationPhage 812 baseplate in the post-contraction state (C1); half map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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-#10
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 / Details: 50mM Tris, 10mM NaCl, 10mM CaCl2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-40 / Number real images: 15371 / Average exposure time: 7.0 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 54841
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

8212

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 21264
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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