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- EMDB-5348: Asymmetric P22 (complete map) -

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Basic information

Entry
Database: EMDB / ID: EMD-5348
TitleAsymmetric P22 (complete map)
Map dataP22 asymmetric
Sample
  • Sample: p22 virus portal protein
  • Virus: Enterobacteria phage P22 (virus)
Keywordsasymmetric reconstruction / phage
Biological speciesEnterobacteria phage P22 (virus)
Methodsingle particle reconstruction / cryo EM
AuthorsTang J / Lander G / Olia A / Li R / Casjens S / Prevelige P / Cingolani G / Baker TS / Johnson JE
CitationJournal: Structure / Year: 2011
Title: Peering down the barrel of a bacteriophage portal: the genome packaging and release valve in p22.
Authors: Jinghua Tang / Gabriel C Lander / Adam S Olia / Rui Li / Sherwood Casjens / Peter Prevelige / Gino Cingolani / Timothy S Baker / John E Johnson /
Abstract: The encapsidated genome in all double-strand DNA bacteriophages is packaged to liquid crystalline density through a unique vertex in the procapsid assembly intermediate, which has a portal protein ...The encapsidated genome in all double-strand DNA bacteriophages is packaged to liquid crystalline density through a unique vertex in the procapsid assembly intermediate, which has a portal protein dodecamer in place of five coat protein subunits. The portal orchestrates DNA packaging and exit, through a series of varying interactions with the scaffolding, terminase, and closure proteins. Here, we report an asymmetric cryoEM reconstruction of the entire P22 virion at 7.8 Å resolution. X-ray crystal structure models of the full-length portal and of the portal lacking 123 residues at the C terminus in complex with gene product 4 (Δ123portal-gp4) obtained by Olia et al. (2011) were fitted into this reconstruction. The interpreted density map revealed that the 150 Å, coiled-coil, barrel portion of the portal entraps the last DNA to be packaged and suggests a mechanism for head-full DNA signaling and transient stabilization of the genome during addition of closure proteins.
History
DepositionOct 26, 2011-
Header (metadata) releaseOct 27, 2011-
Map releaseOct 27, 2011-
UpdateMay 15, 2012-
Current statusMay 15, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5348.map.gz / Format: CCP4 / Size: 564.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationP22 asymmetric
Voxel sizeX=Y=Z: 2.1 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-0.17825823 - 26.803140639999999
Average (Standard dev.)-0.00000001 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-266-266-266
Dimensions533533533
Spacing533533533
CellA=B=C: 1119.2999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.12.12.1
M x/y/z533533533
origin x/y/z0.0000.0000.000
length x/y/z1119.3001119.3001119.300
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-266-266-266
NC/NR/NS533533533
D min/max/mean-0.17826.803-0.000

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Supplemental data

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Sample components

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Entire : p22 virus portal protein

EntireName: p22 virus portal protein
Components
  • Sample: p22 virus portal protein
  • Virus: Enterobacteria phage P22 (virus)

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Supramolecule #1000: p22 virus portal protein

SupramoleculeName: p22 virus portal protein / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Enterobacteria phage P22

SupramoleculeName: Enterobacteria phage P22 / type: virus / ID: 1 / Name.synonym: p22 / NCBI-ID: 10754 / Sci species name: Enterobacteria phage P22 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: p22
Host (natural)synonym: BACTERIA(EUBACTERIA)

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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

VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingDigitization - Sampling interval: 2.1 µm / Number real images: 2888
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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