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- EMDB-27714: Tail of P1 bacteriophage -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-27714
TitleTail of P1 bacteriophage
Map dataTail of P1 bacteriophage
Sample
  • Virus: Escherichia phage P1 (virus)
    • Other: Phage tail protein
Keywordsphage tail / helical / cryo-TEM / CONTRACTILE PROTEIN
Function / homologyGp22
Function and homology information
Biological speciesEscherichia phage P1 (virus)
Methodhelical reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsSen A / Bhatt V / Kim K / Bouchet-Marquis C
Funding support United States, 1 items
OrganizationGrant numberCountry
Other government United States
CitationJournal: To Be Published
Title: Tail of P1 bacteriophage
Authors: Sen A / Bhatt V / Kim K / Bouchet-Marquis C
History
DepositionJul 26, 2022-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27714.png

Downloads & links

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Map

FileDownload / File: emd_27714.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTail of P1 bacteriophage
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 512 pix.
= 355.558 Å		0.69 Å/pix.
x 512 pix.
= 355.558 Å		0.69 Å/pix.
x 512 pix.
= 355.558 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.69445 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.29384196 - 0.50108933
Average (Standard dev.)0.0014945085 (±0.031601034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 355.5584 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map of Tail of P1 bacteriophage

Fileemd_27714_half_map_1.map
Annotationhalf map of Tail of P1 bacteriophage
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of Tail of P1 bacteriophage

Fileemd_27714_half_map_2.map
Annotationhalf map of Tail of P1 bacteriophage
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 P1

EntireName: Escherichia phage P1 (virus)
Components
  • Virus: Escherichia phage P1 (virus)
    • Other: Phage tail protein

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Supramolecule #1: Escherichia phage P1

SupramoleculeName: Escherichia phage P1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2886926 / Sci species name: Escherichia phage P1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Phage tail protein

MacromoleculeName: Phage tail protein / type: other / ID: 1 / Classification: other
Source (natural)Organism: Escherichia phage P1 (virus)
SequenceString: MQRSWFNHRL TSAKQKSLLY KSLADLVQSM MDTFVDPWLE RITN RKSIF SMSKEDLETR TNELGQFFTI RTSNSSSVPM LLQQRLDEIH FKGTERPINQ TIY REFNGI SVLWDPIYAP VDLERHPYGT VLIPESTLET TGGTFGEMFL TSRGMISIPI ND LARTMGI ...String:
MQRSWFNHRL TSAKQKSLLY KSLADLVQSM MDTFVDPWLE RITN RKSIF SMSKEDLETR TNELGQFFTI RTSNSSSVPM LLQQRLDEIH FKGTERPINQ TIY REFNGI SVLWDPIYAP VDLERHPYGT VLIPESTLET TGGTFGEMFL TSRGMISIPI ND LARTMGI TGTIDQSAIT EEILRKFNQF VKPLLPLHIV FDGLTLYLSV VVNEHADMIT L NEISDTEK AYCWFETSDT TSLTGVTSIS APITATPGGT IVKATPTFDR TRADDLLLDS DA

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
GridModel: C-flat-1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average exposure time: 9.4 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 73000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 39.15 Å
Applied symmetry - Helical parameters - Δ&Phi: 19.32 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 119472
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE

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