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- EMDB-2049: Capsid structure and its Stability at the Late Stages of Bacterio... -

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Basic information

Entry
Database: EMDB / ID: EMD-2049
TitleCapsid structure and its Stability at the Late Stages of Bacteriophage SPP1 Assembly
Map dataReconstruction of the full capsid
Sample
  • Sample: Capsid of SPP1
  • Virus: Bacillus phage SPP1 (virus)
KeywordsBacteriophage Capsid SPP1
Function / homologyMajor capsid protein 13-like / Major capsid protein 13-like / T=7 icosahedral viral capsid / viral capsid / Major capsid protein
Function and homology information
Biological speciesBacillus phage SPP1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsWhite HE / Sherman MB / Brasiles S / Jacquet E / Seavers P / Tavares P / Orlova EV
CitationJournal: J Virol / Year: 2012
Title: Capsid structure and its stability at the late stages of bacteriophage SPP1 assembly.
Authors: Helen E White / Michael B Sherman / Sandrine Brasilès / Eric Jacquet / Philippa Seavers / Paulo Tavares / Elena V Orlova /
Abstract: The structure of the bacteriophage SPP1 capsid was determined at subnanometer resolution by cryo-electron microscopy and single-particle analysis. The icosahedral capsid is composed of the major ...The structure of the bacteriophage SPP1 capsid was determined at subnanometer resolution by cryo-electron microscopy and single-particle analysis. The icosahedral capsid is composed of the major capsid protein gp13 and the auxiliary protein gp12, which are organized in a T=7 lattice. DNA is arranged in layers with a distance of ~24.5 Å. gp12 forms spikes that are anchored at the center of gp13 hexamers. In a gp12-deficient mutant, the centers of hexamers are closed by loops of gp13 coming together to protect the SPP1 genome from the outside environment. The HK97-like fold was used to build a pseudoatomic model of gp13. Its structural organization remains unchanged upon tail binding and following DNA release. gp13 exhibits enhanced thermostability in the DNA-filled capsid. A remarkable convergence between the thermostability of the capsid and those of the other virion components was found, revealing that the overall architecture of the SPP1 infectious particle coevolved toward high robustness.
History
DepositionMar 14, 2012-
Header (metadata) releaseMar 23, 2012-
Map releaseJun 14, 2012-
UpdateJun 14, 2012-
Current statusJun 14, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4an5
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4an5
  • Imaged by Jmol
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Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_2049.map.gz / Format: CCP4 / Size: 500 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the full capsid
Voxel sizeX=Y=Z: 1.49 Å
Density
Contour LevelBy AUTHOR: 4.5 / Movie #1: 4.5
Minimum - Maximum-24.62494087 - 32.596717830000003
Average (Standard dev.)0.0 (±2.99999976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-255-256-256
Dimensions512512512
Spacing600600600
CellA=B=C: 894.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.491.491.49
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z894.000894.000894.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-256-255-256
NC/NR/NS512512512
D min/max/mean-24.62532.5970.000

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Supplemental data

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Sample components

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Entire : Capsid of SPP1

EntireName: Capsid of SPP1
Components
  • Sample: Capsid of SPP1
  • Virus: Bacillus phage SPP1 (virus)

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Supramolecule #1000: Capsid of SPP1

SupramoleculeName: Capsid of SPP1 / type: sample / ID: 1000 / Oligomeric state: Icosahedron / Number unique components: 1

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Supramolecule #1: Bacillus phage SPP1

SupramoleculeName: Bacillus phage SPP1 / type: virus / ID: 1 / Details: Coat Protein UniProt ID Q38582 / NCBI-ID: 10724 / Sci species name: Bacillus phage SPP1 / Virus type: OTHER / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Bacillus subtilis (bacteria) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Diameter: 600 Å / T number (triangulation number): 7

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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

GridDetails: holey carbon film grids
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeJEOL 2200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Detailslow-dose imaging procedure
DateApr 6, 2005
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 94 / Average electron dose: 20 e/Å2

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Image processing

CTF correctionDetails: Phase flipping
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic / Number images used: 5000

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Atomic model buiding 1

Initial modelPDB ID:
SoftwareName: Flex-EM
DetailsProtocol: Each helix and every beta sheet were treated as rigid bodies.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4an5:
Capsid structure and its Stability at the Late Stages of Bacteriophage SPP1 Assembly

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