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- EMDB-22513: Satellite phage P4 procapsid including size determination (Sid) p... -

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Basic information

Entry
Database: EMDB / ID: EMD-22513
TitleSatellite phage P4 procapsid including size determination (Sid) protein
Map data
SampleP4 procapsid:
Major capsid protein gpN / Size determination protein Sid
Function / homologyBacteriophage P2, GpN, major capsid / viral capsid / Glycoprotein 3 / Capsid proteins
Function and homology information
Biological speciesEscherichia coli (E. coli) / Escherichia phage P2 (bacteriophage) / Enterobacteria phage P4 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.19 Å
AuthorsKizziah JL / Dokland T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI083255 United States
CitationJournal: Viruses / Year: 2020
Title: Structure of the Capsid Size-Determining Scaffold of "Satellite" Bacteriophage P4.
Authors: James L Kizziah / Cynthia M Rodenburg / Terje Dokland /
Abstract: P4 is a mobile genetic element (MGE) that can exist as a plasmid or integrated into its host genome, but becomes packaged into phage particles by a helper bacteriophage, such as P2. P4 is the ...P4 is a mobile genetic element (MGE) that can exist as a plasmid or integrated into its host genome, but becomes packaged into phage particles by a helper bacteriophage, such as P2. P4 is the original example of what we have termed "molecular piracy", the process by which one MGE usurps the life cycle of another for its own propagation. The P2 helper provides most of the structural gene products for assembly of the P4 virion. However, when P4 is mobilized by P2, the resulting capsids are smaller than those normally formed by P2 alone. The P4-encoded protein responsible for this size change is called Sid, which forms an external scaffolding cage around the P4 procapsids. We have determined the high-resolution structure of P4 procapsids, allowing us to build an atomic model for Sid as well as the gpN capsid protein. Sixty copies of Sid form an intertwined dodecahedral cage around the = 4 procapsid, making contact with only one out of the four symmetrically non-equivalent copies of gpN. Our structure provides a basis for understanding the mutants in gpN that prevent small capsid formation, as well as the "super-sid" mutations that counteract the effect of the mutations, and suggests a model for capsid size redirection by Sid.
Validation ReportPDB-ID: 7jw1

SummaryFull reportAbout validation report
History
DepositionAug 24, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateSep 23, 2020-
Current statusSep 23, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jw1
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7jw1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_22513.map.gz / Format: CCP4 / Size: 2.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 864 pix.
= 959.04 Å
1.11 Å/pix.
x 864 pix.
= 959.04 Å
1.11 Å/pix.
x 864 pix.
= 959.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density
Contour LevelBy AUTHOR: 5 / Movie #1: 5
Minimum - Maximum-21.576601 - 39.08183
Average (Standard dev.)0.0000000732 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions864864864
Spacing864864864
CellA=B=C: 959.04004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z864864864
origin x/y/z0.0000.0000.000
length x/y/z959.040959.040959.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS864864864
D min/max/mean-21.57739.0820.000

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Supplemental data

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Segmentation: #1

Fileemd_22513_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map 1 from auto-refinement of final map.

Fileemd_22513_half_map_1.map
AnnotationHalf map 1 from auto-refinement of final map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map 2 from auto-refinement of final map.

Fileemd_22513_half_map_2.map
AnnotationHalf map 2 from auto-refinement of final map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire P4 procapsid

EntireName: P4 procapsid / Number of components: 3

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Component #1: protein, P4 procapsid

ProteinName: P4 procapsid / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli) / Strain: BL21(DE3)

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Component #2: protein, Major capsid protein gpN

ProteinName: Major capsid protein gpN / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 40.291484 kDa
SourceSpecies: Escherichia phage P2 (bacteriophage)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Size determination protein Sid

ProteinName: Size determination protein Sid / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.296814 kDa
SourceSpecies: Enterobacteria phage P4 (bacteriophage)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 438018
3D reconstructionResolution: 4.19 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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