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- EMDB-27595: Cryo-EM structure of tail machine from del7.3K2R1 with empty caps... -

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Basic information

Entry
Database: EMDB / ID: EMD-27595
TitleCryo-EM structure of tail machine from del7.3K2R1 with empty capsid and opened tail
Map data
Sample
  • Complex: Tail machine in mature bacteriophage T7
KeywordsT7 / tail machine / adsorption / genome ejection / VIRUS
Function / homology
Function and homology information


host cell periplasmic space / virus tail, tube / viral portal complex / virus tail, fiber / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / adhesion receptor-mediated virion attachment to host cell / virion component / symbiont entry into host cell / virion attachment to host cell ...host cell periplasmic space / virus tail, tube / viral portal complex / virus tail, fiber / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / adhesion receptor-mediated virion attachment to host cell / virion component / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / identical protein binding / membrane
Similarity search - Function
Internal virion protein Gp14 / : / Tail fibre protein gp37 trimerization region / Bacteriophage T7, Gp17, C-terminal / Internal virion protein Gp15 / Tail fibre protein gp37 C terminal domain / Tail tubular protein Gp11 / Tail tubular protein / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein ...Internal virion protein Gp14 / : / Tail fibre protein gp37 trimerization region / Bacteriophage T7, Gp17, C-terminal / Internal virion protein Gp15 / Tail fibre protein gp37 C terminal domain / Tail tubular protein Gp11 / Tail tubular protein / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein / Portal protein, Caudovirales / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein
Similarity search - Domain/homology
Internal virion protein gp14 / Internal virion protein gp15 / Portal protein / Tail tubular protein gp11 / Tail tubular protein gp12 / Tail fiber protein
Similarity search - Component
Biological speciesEscherichia phage T7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang C / Liu J / Molineux IJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Virion remodeling of bacteriophage T7 during infection initiation
Authors: Wang C / Park T / Liu J / Molineux IJ
History
DepositionJul 12, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateJul 19, 2023-
Current statusJul 19, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27595.png

Downloads & links

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Map

FileDownload / File: emd_27595.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 427.2 Å		1.07 Å/pix.
x 400 pix.
= 427.2 Å		1.07 Å/pix.
x 400 pix.
= 427.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.012198287 - 0.025635596
Average (Standard dev.)0.00019695505 (±0.0013884101)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 427.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_27595_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_27595_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tail machine in mature bacteriophage T7

EntireName: Tail machine in mature bacteriophage T7
Components
  • Complex: Tail machine in mature bacteriophage T7

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Supramolecule #1: Tail machine in mature bacteriophage T7

SupramoleculeName: Tail machine in mature bacteriophage T7 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia phage T7 (virus)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29784
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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