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- EMDB-18385: Consensus density for neck and tail of phage 812 after tail contr... -

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Basic information

Entry
Database: EMDB / ID: EMD-18385
TitleConsensus density for neck and tail of phage 812 after tail contraction (C6)
Map dataConsensus density for neck and tail of phage 812 after tail contraction (C6)
Sample
  • Virus: Staphylococcus phage 812 (virus)
Keywordsphage / neck / tail / connector / VIRUS
Biological speciesStaphylococcus phage 812 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.23 Å
AuthorsCienikova Z / Siborova M / Fuzik T / Plevka P
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech Republic Czech Republic
CitationJournal: To Be Published
Title: Genome anchoring, retention, and release by neck proteins of Herelleviridae phage 812
Authors: Cienikova Z / Novacek J / Siborova M / Popelarova B / Fuzik T / Benesik M / Bardy P / Plevka P
History
DepositionSep 5, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18385.png

Downloads & links

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Map

FileDownload / File: emd_18385.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus density for neck and tail of phage 812 after tail contraction (C6)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.11 Å/pix.
x 288 pix.
= 608.832 Å		2.11 Å/pix.
x 288 pix.
= 608.832 Å		2.11 Å/pix.
x 288 pix.
= 608.832 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.114 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.023
Minimum - Maximum-0.0592911 - 0.15086158
Average (Standard dev.)0.0020305691 (±0.008401189)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 608.83203 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map 1

Fileemd_18385_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_18385_half_map_2.map
AnnotationHalf-map 2
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 812

EntireName: Staphylococcus phage 812 (virus)
Components
  • Virus: Staphylococcus phage 812 (virus)

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Supramolecule #1: Staphylococcus phage 812

SupramoleculeName: Staphylococcus phage 812 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Purified phage virion was incubated in urea and LTA to induce tail contraction and genome ejection
NCBI-ID: 307898 / Sci species name: Staphylococcus phage 812 / Sci species strain: K1-420 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Staphylococcus aureus (bacteria) / Strain: CCM 8428
Virus shellShell ID: 1 / Diameter: 1100.0 Å

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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 mMC4H11NO3Tris
10.0 mMNaClsodium chloride
10.0 mMCaClcalcium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
DetailsPhage viral particles after tail contraction in urea and lipo-teichoic acid, buffer-exchanged by centrifugation.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 1 / 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: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 130000
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

DetailsFrame alignment and dose-weighting with MotionCor2, then contrast inversion and normalization
Particle selectionNumber selected: 32222
Details: Particle selection using cross-correlation against capsid template
Startup modelType of model: EMDB MAP
EMDB ID:

8209

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 17304
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Details: Selection of particles without genome in the capsid, and aligned on capsid and neck.
FSC plot (resolution estimation)

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