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- EMDB-55786: Bacteriophage 812 head filled with DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-55786
TitleBacteriophage 812 head filled with DNA
Map dataPhage 812 head filled with DNA
Sample
  • Virus: Staphylococcus phage 812K1/420 (virus)
KeywordsBacterophage / phage cycle / capsid assembly / sub-tomogram averaging / Herelleviridae / VIRUS
Biological speciesStaphylococcus phage 812K1/420 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 30.21 Å
AuthorsZlatohurska M / Prochazkova M / Fuzik T / Plevka P
Funding supportEuropean Union, Czech Republic, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)101043452European Union
Ministry of Education, Youth and Sports of the Czech RepublicLX22NPO5103 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.01.01/00/22_008/0004607 Czech Republic
European Research Council (ERC)1233487European Union
CitationJournal: To Be Published
Title: Cryo-ET of S. aureus infection by Herelleviridae phage 812
Authors: Prochazkova M / Zlatohurska M / Cienikova Z / Fuzik T / Bardy P / Pantucek R / Plevka P
History
DepositionNov 21, 2025-
Header (metadata) releaseOct 28, 2026-
Map releaseOct 28, 2026-
UpdateOct 28, 2026-
Current statusOct 28, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55786.png

Downloads & links

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Map

FileDownload / File: emd_55786.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhage 812 head filled with DNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.81 Å/pix.
x 144 pix.
= 1268.928 Å		8.81 Å/pix.
x 144 pix.
= 1268.928 Å		8.81 Å/pix.
x 144 pix.
= 1268.928 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.812 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0634
Minimum - Maximum-0.021117717 - 0.08216425
Average (Standard dev.)0.013419635 (±0.022773974)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144144144
Spacing144144144
CellA=B=C: 1268.928 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55786_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The EM half map was calculated using RELION 4.

Fileemd_55786_half_map_1.map
AnnotationThe EM half map was calculated using RELION 4.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The EM half map was calculated using RELION 4.

Fileemd_55786_half_map_2.map
AnnotationThe EM half map was calculated using RELION 4.
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 / NCBI-ID: 3434241 / Sci species name: Staphylococcus phage 812K1/420 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Staphylococcus aureus (bacteria)
Virus shellShell ID: 1 / Name: capsid / Diameter: 900.0 Å

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.9
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsThe phage 812-infected S. aureus cells have been plunge-frozen and thinned using focused-ion-beam milling.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 33000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 30.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 344
ExtractionNumber tomograms: 18 / Number images used: 809 / Software - Name: emClarity
CTF correctionSoftware - Name: emClarity / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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