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- EMDB-5201: The electron cryo-microscopic structure of Shigella phage Sf6 rev... -

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Basic information

Entry
Database: EMDB / ID: EMD-5201
TitleThe electron cryo-microscopic structure of Shigella phage Sf6 reveals novel cementing proteins
Map dataElectron cryo-microscopic reconstruction of Shigella phage Sf6. The image is viewed approximately down the icosahedral 3-fold axis, and an octant of the capsid was removed to show the internal density (colored in green) that corresponds to the two host-derived cementing proteins.
Sample
  • Sample: bacteriophage Sf6
  • Virus: Bacillus phage SF6 (virus)
Keywordsvirus assembly / cementing protein / bacteriophage / Sf6 / Shigella
Function / homology
Function and homology information


outer membrane protein complex / monoatomic ion transmembrane transporter activity / detection of virus / outer membrane / porin activity / pore complex / monoatomic ion transport / monoatomic ion transmembrane transport / cell outer membrane / virus receptor activity ...outer membrane protein complex / monoatomic ion transmembrane transporter activity / detection of virus / outer membrane / porin activity / pore complex / monoatomic ion transport / monoatomic ion transmembrane transport / cell outer membrane / virus receptor activity / outer membrane-bounded periplasmic space / receptor-mediated virion attachment to host cell / symbiont entry into host cell / DNA damage response / membrane / identical protein binding / metal ion binding
Similarity search - Function
Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin ...Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin, Gram-negative type / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / Porin domain superfamily / Outer membrane protein/outer membrane enzyme PagP, beta-barrel
Similarity search - Domain/homology
Outer membrane porin C / Outer membrane protein A
Similarity search - Component
Biological speciesBacillus phage SF6 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 19.0 Å
AuthorsZhao H / Sequeira RD / Galeva NA / Tang L
CitationJournal: Virology / Year: 2011
Title: The host outer membrane proteins OmpA and OmpC are associated with the Shigella phage Sf6 virion.
Authors: Haiyan Zhao / Reuben D Sequeira / Nadezhda A Galeva / Liang Tang /
Abstract: Assembly of dsDNA bacteriophage is a precisely programmed process. Potential roles of host cell components in phage assembly haven't been well understood. It was previously reported that two ...Assembly of dsDNA bacteriophage is a precisely programmed process. Potential roles of host cell components in phage assembly haven't been well understood. It was previously reported that two unidentified proteins were present in bacteriophage Sf6 virion (Casjens et al, 2004, J.Mol.Biol. 339, 379-394, Fig. 2A). Using tandem mass spectrometry, we have identified the two proteins as outer membrane proteins (OMPs) OmpA and OmpC from its host Shigella flexneri. The transmission electron cryo-microscopy structure of Sf6 shows significant density at specific sites at the phage capsid inner surface. This density fit well with the characteristic beta-barrel domains of OMPs, thus may be due to the two host proteins. Locations of this density suggest a role in Sf6 morphogenesis reminiscent of phage-encoded cementing proteins. These data indicate a new, OMP-related phage:host linkage, adding to previous knowledge that some lambdoid bacteriophage genomes contain OmpC-like genes that express phage-encoded porins in the lysogenic state.
History
DepositionJun 1, 2010-
Header (metadata) releaseJul 14, 2010-
Map releaseFeb 7, 2011-
UpdateFeb 7, 2011-
Current statusFeb 7, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.25
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3nb3
  • Surface level: 1.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3nb3
  • Surface level: 1.25
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3nb3
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5201_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5201.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationElectron cryo-microscopic reconstruction of Shigella phage Sf6. The image is viewed approximately down the icosahedral 3-fold axis, and an octant of the capsid was removed to show the internal density (colored in green) that corresponds to the two host-derived cementing proteins.
Voxel sizeX=Y=Z: 3.9284 Å
Density
Contour LevelBy AUTHOR: 1.25 / Movie #1: 1.25
Minimum - Maximum-4.86976 - 4.75651
Average (Standard dev.)-0.0191559 (±1.00096)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-99-99-99
Dimensions200200200
Spacing200200200
CellA=B=C: 785.68 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.92843.92843.9284
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z785.680785.680785.680
α/β/γ90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S213
start NC/NR/NS-99-99-99
NC/NR/NS200200200
D min/max/mean-4.8704.757-0.019

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Supplemental data

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Sample components

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Entire : bacteriophage Sf6

EntireName: bacteriophage Sf6 (virus)
Components
  • Sample: bacteriophage Sf6
  • Virus: Bacillus phage SF6 (virus)

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Supramolecule #1000: bacteriophage Sf6

SupramoleculeName: bacteriophage Sf6 / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 60
Molecular weightTheoretical: 19.2 MDa

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Supramolecule #1: Bacillus phage SF6

SupramoleculeName: Bacillus phage SF6 / type: virus / ID: 1 / Name.synonym: Sf6 / Details: purified infectious virion / NCBI-ID: 10773 / Sci species name: Bacillus phage SF6 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: Sf6
Host (natural)Organism: Shigella flexneri (bacteria) / synonym: BACTERIA(EUBACTERIA)
Molecular weightTheoretical: 19.2 MDa
Virus shellShell ID: 1 / Name: gp5 / Diameter: 680 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

Concentration2 mg/mL
BufferpH: 7.4 / Details: 10 mM Tric-HCl, pH 7.4, 10mM MgCl2
GridDetails: 300 mech holey copper grid
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: home-made plunger / Method: blot for 3-4 seconds before plunging

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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 / Nominal defocus max: 1.06 µm / Nominal defocus min: 0.471 µm / Nominal magnification: 39000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 89 K
Image recordingCategory: CCD / Film or detector model: GENERIC CCD (2k x 2k) / Number real images: 79 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final angle assignmentDetails: SPIDER: theta 31.72, phi 180
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 3232

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Atomic model buiding 1

Initial modelPDB ID:

1qjp


Chain - Chain ID: A
DetailsPDBEntryID_givenInChain. The coordinates were fitted by manual docking using program O and UCSF Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3nb3:
The host outer membrane proteins OmpA and OmpC are packed at specific sites in the Shigella phage Sf6 virion as structural components

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Atomic model buiding 2

Initial modelPDB ID:

2j1n


Chain - Chain ID: A
DetailsPDBEntryID_givenInChain. The coordinates were fitted by manual docking using program O and UCSF Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3nb3:
The host outer membrane proteins OmpA and OmpC are packed at specific sites in the Shigella phage Sf6 virion as structural components

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