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- EMDB-35127: The asymmetry unit of P22 empty procapsid -

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Basic information

Entry
Database: EMDB / ID: EMD-35127
TitleThe asymmetry unit of P22 empty procapsid
Map data
Sample
  • Virus: Salmonella phage P22 (virus)
KeywordsComplex / VIRUS
Biological speciesSalmonella phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsXiao H / Liu HR / Cheng LP
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)31971122 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)32200994 China
CitationJournal: Viruses / Year: 2023
Title: Assembly and Capsid Expansion Mechanism of Bacteriophage P22 Revealed by High-Resolution Cryo-EM Structures
Authors: Xiao H / Zhou J / Yang F / Liu Z / Song J / Chen W / Liu H / Cheng L
History
DepositionJan 13, 2023-
Header (metadata) releaseMar 8, 2023-
Map releaseMar 8, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35127.png

Downloads & links

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Map

FileDownload / File: emd_35127.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-19.674188999999998 - 34.139969999999998
Average (Standard dev.)0.006992476 (±1.448467)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-340-340-340
Dimensions360360360
Spacing360360360
CellA=B=C: 381.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35127_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35127_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 : Salmonella phage P22

EntireName: Salmonella phage P22 (virus)
Components
  • Virus: Salmonella phage P22 (virus)

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Supramolecule #1: Salmonella phage P22

SupramoleculeName: Salmonella phage P22 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 2908168 / Sci species name: Salmonella phage P22 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes

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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: 7.4
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: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70140
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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