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- EMDB-48462: 6-fold-symmetric reconstruction focused on the bacteriophage T4 n... -

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Basic information

Entry
Database: EMDB / ID: EMD-48462
Title6-fold-symmetric reconstruction focused on the bacteriophage T4 neck region
Map data6-fold-symmetric reconstruction focused on the bacteriophage T4 neck region
Sample
  • Virus: Escherichia phage T4 (virus)
Keywordsbacteriophage T4 / portal vertex / phage neck / tail terminator protein / tube terminator protein / asymmetric phage reconstruction / DNA retention / neck stopper protein / head completion proteins / VIRUS
Biological speciesEscherichia phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsFokine A / Zhu J / Klose T / Vago F / Arnaud C / Wang Z / Khare B / Rossmann MG / Chen Z / Sun L ...Fokine A / Zhu J / Klose T / Vago F / Arnaud C / Wang Z / Khare B / Rossmann MG / Chen Z / Sun L / Fang Q / Kuhn R / Rao VB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081726 United States
CitationJournal: To Be Published
Title: In situ Atomic Structure of Phage T4 Head-Tail Connector Complex Shows Molecular Gates Open for Genome Ejection and DNA Pushed into the Tail Tube
Authors: Fokine A / Zhu J / Klose T / Vago F / Arnaud C / Wang Z / Khare B / Rossmann MG / Chen Z / Sun L / Fang Q / Kuhn R / Rao VB
History
DepositionDec 26, 2024-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48462.png

Downloads & links

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Map

FileDownload / File: emd_48462.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation6-fold-symmetric reconstruction focused on the bacteriophage T4 neck region
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.62 Å/pix.
x 400 pix.
= 646.4 Å		1.62 Å/pix.
x 400 pix.
= 646.4 Å		1.62 Å/pix.
x 400 pix.
= 646.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.616 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.07326812 - 0.12258646
Average (Standard dev.)-0.00003214256 (±0.004318131)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 646.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48462_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_48462_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_48462_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia phage T4

EntireName: Escherichia phage T4 (virus)
Components
  • Virus: Escherichia phage T4 (virus)

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Supramolecule #1: Escherichia phage T4

SupramoleculeName: Escherichia phage T4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#12 / NCBI-ID: 2681598 / Sci species name: Escherichia phage T4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli) / Strain: B

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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: 7.5
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Support film - Material: CARBON / Support film - topology: LACEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Ted Pella lacey carbon 400 mesh grids (catalog No: 01824) were used..

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 38.0 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: 0.6 µm
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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 164000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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