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- EMDB-27657: Cryo-EM structure of proximal fiber in del7.3K2R1 free phage -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-27657
TitleCryo-EM structure of proximal fiber in del7.3K2R1 free phage
Map data
Sample
  • Virus: Escherichia phage T7 (virus)
KeywordsBacteriophage T7 / VIRUS
Function / homology
Function and homology information


virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell / virion attachment to host cell / identical protein binding
Similarity search - Function
: / Tail fibre protein gp37 trimerization region / Bacteriophage T7, Gp17, C-terminal / Tail fibre protein gp37 C terminal domain / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein, N-terminal domain
Similarity search - Domain/homology
Biological speciesEscherichia phage T7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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: Asymmetric reconstruction of gp8-gp11 with terminal dsDNA associated from the del7.3K2R1.
Authors: Wang C / Liu J / Molineux IJ
History
DepositionJul 19, 2022-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateFeb 7, 2024-
Current statusFeb 7, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27657.png

Downloads & links

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Map

FileDownload / File: emd_27657.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-0.016949292 - 0.04175522
Average (Standard dev.)0.000011474473 (±0.00044030996)
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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Additional map: unmasked average

Fileemd_27657_additional_1.map
Annotationunmasked average
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27657_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_27657_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 : Escherichia phage T7

EntireName: Escherichia phage T7 (virus)
Components
  • Virus: Escherichia phage T7 (virus)

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Supramolecule #1: Escherichia phage T7

SupramoleculeName: Escherichia phage T7 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10760 / Sci species name: Escherichia phage T7 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / 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: 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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99318
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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