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- EMDB-1482: Structrue of truncated portal(portal602) complex with gp4 from ba... -

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Basic information

Entry
Database: EMDB / ID: EMD-1482
TitleStructrue of truncated portal(portal602) complex with gp4 from bacteriophage P22
Map datamap of portal602 complex with gp4
Sample
  • Sample: truncated portal complex with gp4 from bacteriophage P22
  • Protein or peptide: gp1, gp4
Biological speciesEnterobacteria phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.5 Å
AuthorsZheng H / Olia AS / Gonen M / Andrews S / Cingolani G / Gonen T
CitationJournal: Mol Cell / Year: 2008
Title: A conformational switch in bacteriophage p22 portal protein primes genome injection.
Authors: Hongjin Zheng / Adam S Olia / Melissa Gonen / Simeon Andrews / Gino Cingolani / Tamir Gonen /
Abstract: Double-stranded DNA (dsDNA) viruses such as herpesviruses and bacteriophages infect by delivering their genetic material into cells, a task mediated by a DNA channel called "portal protein." We have ...Double-stranded DNA (dsDNA) viruses such as herpesviruses and bacteriophages infect by delivering their genetic material into cells, a task mediated by a DNA channel called "portal protein." We have used electron cryomicroscopy to determine the structure of bacteriophage P22 portal protein in both the procapsid and mature capsid conformations. We find that, just as the viral capsid undergoes major conformational changes during virus maturation, the portal protein switches conformation from a procapsid to a mature phage state upon binding of gp4, the factor that initiates tail assembly. This dramatic conformational change traverses the entire length of the DNA channel, from the outside of the virus to the inner shell, and erects a large dome domain directly above the DNA channel that binds dsDNA inside the capsid. We hypothesize that this conformational change primes dsDNA for injection and directly couples completion of virus morphogenesis to a new cycle of infection.
History
DepositionFeb 26, 2008-
Header (metadata) releaseFeb 26, 2008-
Map releaseMar 31, 2009-
UpdateDec 25, 2013-
Current statusDec 25, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.850629391
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3.850629391
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1482.gif

Downloads & links

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Map

FileDownload / File: emd_1482.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of portal602 complex with gp4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.48 Å/pix.
x 120 pix.
= 297.6 Å		2.48 Å/pix.
x 120 pix.
= 297.6 Å		2.48 Å/pix.
x 120 pix.
= 297.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.48 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 2.75 / Movie #1: 3.8506294
Minimum - Maximum-2.59705 - 7.69801
Average (Standard dev.)-0.00000000713014 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-60-60-60
Dimensions120120120
Spacing120120120
CellA=B=C: 297.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.482.482.48
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z297.600297.600297.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-55-55-55
NX/NY/NZ111111111
MAP C/R/S123
start NC/NR/NS-60-60-60
NC/NR/NS120120120
D min/max/mean-2.5977.698-0.000

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Supplemental data

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Sample components

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Entire : truncated portal complex with gp4 from bacteriophage P22

EntireName: truncated portal complex with gp4 from bacteriophage P22
Components
  • Sample: truncated portal complex with gp4 from bacteriophage P22
  • Protein or peptide: gp1, gp4

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Supramolecule #1000: truncated portal complex with gp4 from bacteriophage P22

SupramoleculeName: truncated portal complex with gp4 from bacteriophage P22
type: sample / ID: 1000 / Oligomeric state: 12mer of portal with 12mer of gp4 / Number unique components: 2

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Macromolecule #1: gp1, gp4

MacromoleculeName: gp1, gp4 / type: protein_or_peptide / ID: 1 / Name.synonym: gp1, gp4 / Recombinant expression: Yes
Source (natural)Organism: Enterobacteria phage P22 (virus)

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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: OTHER / Imaging mode: OTHER
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF

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