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- EMDB-1020: Structure of a viral DNA gatekeeper at 10 A resolution by cryo-el... -

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Basic information

Entry
Database: EMDB / ID: EMD-1020
TitleStructure of a viral DNA gatekeeper at 10 A resolution by cryo-electron microscopy.
Map dataViral DNA gatekeeper. Centre of symmetry : 50.0, 50.0, 50.0
Sample
  • Sample: Bacteriophage SPP1 portal protein gp6
  • Protein or peptide: Bacteriophage SPP1 portal protein gp6
Biological speciesBacillus phage SPP1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsOrlova EV / Gowen B / Droege A / Stiege A / Weise F / Lurz R / van Heel M / Tavares P
CitationJournal: EMBO J / Year: 2003
Title: Structure of a viral DNA gatekeeper at 10 A resolution by cryo-electron microscopy.
Authors: Elena V Orlova / Brent Gowen / Anja Dröge / Asita Stiege / Frank Weise / Rudi Lurz / Marin van Heel / Paulo Tavares /
Abstract: In tailed bacteriophages and herpes viruses, the viral DNA is packaged through the portal protein channel. Channel closure is essential to prevent DNA release after packaging. Here we present the ...In tailed bacteriophages and herpes viruses, the viral DNA is packaged through the portal protein channel. Channel closure is essential to prevent DNA release after packaging. Here we present the connector structure from bacteriophage SPP1 using cryo-electron microscopy and single particle analysis. The multiprotein complex comprises the portal protein gp6 and the head completion proteins gp15 and gp16. Although we show that gp6 in the connector has a fold similar to that of the isolated portal protein, we observe conformational changes in the region of gp6 exposed to the DNA-packaging ATPase and to gp15. This reorganization does not cause closure of the channel. The connector channel traverses the full height of gp6 and gp15, but it is closed by gp16 at the bottom of the complex. Gp16 acts as a valve whose closure prevents DNA leakage, while its opening is required for DNA release upon interaction of the virus with its host.
History
DepositionJan 31, 2003-
Header (metadata) releaseJan 31, 2003-
Map releaseMar 31, 2003-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0627
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0627
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2jes
  • Surface level: 0.0627
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1020.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationViral DNA gatekeeper. Centre of symmetry : 50.0, 50.0, 50.0
Voxel sizeX=Y=Z: 2.1 Å
Density
Contour Level1: 0.0874 / Movie #1: 0.0627
Minimum - Maximum-0.189776 - 0.296457
Average (Standard dev.)0.0039891 (±0.0396917)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 210 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.12.12.1
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z210.000210.000210.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.1900.2960.004

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Supplemental data

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Sample components

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Entire : Bacteriophage SPP1 portal protein gp6

EntireName: Bacteriophage SPP1 portal protein gp6
Components
  • Sample: Bacteriophage SPP1 portal protein gp6
  • Protein or peptide: Bacteriophage SPP1 portal protein gp6

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Supramolecule #1000: Bacteriophage SPP1 portal protein gp6

SupramoleculeName: Bacteriophage SPP1 portal protein gp6 / type: sample / ID: 1000
Oligomeric state: isolated portal protein has 13- fold cyclical symmetry
Number unique components: 1
Molecular weightExperimental: 57.3 KDa / Theoretical: 57.3 KDa

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Macromolecule #1: Bacteriophage SPP1 portal protein gp6

MacromoleculeName: Bacteriophage SPP1 portal protein gp6 / type: protein_or_peptide / ID: 1 / Name.synonym: naive gp6 / Number of copies: 13 / Oligomeric state: C13 / Recombinant expression: Yes
Source (natural)Organism: Bacillus phage SPP1 (virus) / synonym: Bacteriophage SPP1
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: Pbluescript SK+ + pLysS

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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

Concentration1.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Standard plunger / Method: Blot about 2-3 seconds before plunging.

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG/ST
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 48600 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.1 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 50000
Sample stageSpecimen holder: side-entry / Specimen holder model: GATAN LIQUID NITROGEN
DateJan 1, 1999
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PATCHWORK DENSITOMETER / Digitization - Sampling interval: 10.2 µm / Number real images: 15 / Average electron dose: 10 e/Å2
Details: Images were digitised using a patch work densitometer.
Od range: 1.6 / Bits/pixel: 8

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Image processing

CTF correctionDetails: CTF correction of each particle
Final two d classificationNumber classes: 430
Final reconstructionApplied symmetry - Point group: C13 (13 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: OTHER / Software - Name: IMAGIC / Number images used: 8000
DetailsThe number of classes analysed was 650. In the final reconstruction were used only 430.

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Atomic model buiding 1

SoftwareName: Molrep
DetailsProtocol: Angular reconstitution

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