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- EMDB-7317: P22 gp26minus asymmetric reconstruction C12 symmetry along Z-axis -

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Basic information

Entry
Database: EMDB / ID: EMD-7317
TitleP22 gp26minus asymmetric reconstruction C12 symmetry along Z-axis
Map dataBacteriophage P22 asymmetric reconstruction 12-fold symmetry along Z-axis
Sample
  • Virus: Enterobacteria phage P22 (virus)
Biological speciesEnterobacteria phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.5 Å
AuthorsMcNulty R / Johnson JE
CitationJournal: Biophys J / Year: 2018
Title: Cryo-EM Elucidation of the Structure of Bacteriophage P22 Virions after Genome Release.
Authors: Reginald McNulty / Giovanni Cardone / Eddie B Gilcrease / Timothy S Baker / Sherwood R Casjens / John E Johnson /
Abstract: Genome ejection proteins are required to facilitate transport of bacteriophage P22 double-stranded DNA safely through membranes of Salmonella. The structures and locations of all proteins in the ...Genome ejection proteins are required to facilitate transport of bacteriophage P22 double-stranded DNA safely through membranes of Salmonella. The structures and locations of all proteins in the context of the mature virion are known, with the exception of three ejection proteins. Furthermore, the changes that occur to the proteins residing in the mature virion upon DNA release are not fully understood. We used cryogenic electron microscopy to obtain what is, to our knowledge, the first asymmetric reconstruction of mature bacteriophage P22 after double-stranded DNA has been extruded from the capsid-a state representative of one step during viral infection. Results of icosahedral and asymmetric reconstructions at estimated resolutions of 7.8 and 12.5 Å resolutions, respectively, are presented. The reconstruction shows tube-like protein density extending from the center of the tail assembly. The portal protein does not revert to the more contracted, procapsid state, but instead maintains an extended and splayed barrel structure. These structural details contribute to our understanding of the molecular mechanism of P22 phage infection and also set the foundation for future exploitation serving engineering purposes.
History
DepositionDec 24, 2017-
Header (metadata) releaseJan 24, 2018-
Map releaseApr 18, 2018-
UpdateApr 18, 2018-
Current statusApr 18, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 10
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7317.png

Downloads & links

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Map

FileDownload / File: emd_7317.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacteriophage P22 asymmetric reconstruction 12-fold symmetry along Z-axis
Voxel sizeX=Y=Z: 1.58 Å
Density
Contour LevelBy AUTHOR: 5.28 / Movie #1: 10
Minimum - Maximum-109.457790000000003 - 76.274154999999993
Average (Standard dev.)0.005912567 (±5.901588)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-400-400-400
Dimensions800800800
Spacing800800800
CellA=B=C: 1264.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.581.581.58
M x/y/z800800800
origin x/y/z0.0000.0000.000
length x/y/z1264.0001264.0001264.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-128-128-128
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS-400-400-400
NC/NR/NS800800800
D min/max/mean-109.45876.2740.006

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Supplemental data

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Sample components

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Entire : Enterobacteria phage P22

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

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Supramolecule #1: Enterobacteria phage P22

SupramoleculeName: Enterobacteria phage P22 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10754 / Sci species name: Enterobacteria phage P22 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host systemOrganism: Salmonella enterica (bacteria)

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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 TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Average electron dose: 57.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing #1

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2xyz


Details: Low pass-filtered to 50 angstroms
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: FREALIGN (ver. 9.11)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: Auto3DEM (ver. 4.05.2)
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 12.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: Auto3DEM (ver. 4.05.2), EMAN2 (ver. 2.2)) / Number images used: 1935
Image processing ID1

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Image processing #2

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2xyz


Details: low pass-filtered to 50 angstroms
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 12.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1935
Image processing ID2

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Image processing #3

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2xyz

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 12.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: Auto3DEM (ver. 4.05.2), EMAN2 (ver. 2.2)) / Number images used: 1935
Image processing ID3

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