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Yorodumi- EMDB-1020: Structure of a viral DNA gatekeeper at 10 A resolution by cryo-el... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1020 | |||||||||
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Title | Structure of a viral DNA gatekeeper at 10 A resolution by cryo-electron microscopy. | |||||||||
Map data | Viral DNA gatekeeper. Centre of symmetry : 50.0, 50.0, 50.0 | |||||||||
Sample |
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Biological species | Bacillus phage SPP1 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.0 Å | |||||||||
Authors | Orlova EV / Gowen B / Droege A / Stiege A / Weise F / Lurz R / van Heel M / Tavares P | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1020.map.gz | 1.3 MB | EMDB map data format | |
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Header (meta data) | emd-1020-v30.xml emd-1020.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | 1020.gif emd_1020.tif emd_emd_1020.tif | 23.5 KB 588.8 KB 588.8 KB | ||
Others | Resolution_Portal_Connector.tif | 143.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1020 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1020 | HTTPS FTP |
-Validation report
Summary document | emd_1020_validation.pdf.gz | 235 KB | Display | EMDB validaton report |
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Full document | emd_1020_full_validation.pdf.gz | 234.1 KB | Display | |
Data in XML | emd_1020_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1020 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1020 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1020.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Viral DNA gatekeeper. Centre of symmetry : 50.0, 50.0, 50.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Others
-Sample components
-Entire : Bacteriophage SPP1 portal protein gp6
Entire | Name: Bacteriophage SPP1 portal protein gp6 |
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Components |
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-Supramolecule #1000: Bacteriophage SPP1 portal protein gp6
Supramolecule | Name: Bacteriophage SPP1 portal protein gp6 / type: sample / ID: 1000 Oligomeric state: isolated portal protein has 13- fold cyclical symmetry Number unique components: 1 |
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Molecular weight | Experimental: 57.3 KDa / Theoretical: 57.3 KDa |
-Macromolecule #1: Bacteriophage SPP1 portal protein gp6
Macromolecule | Name: 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 |
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Source (natural) | Organism: Bacillus phage SPP1 (virus) / synonym: Bacteriophage SPP1 |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: Pbluescript SK+ + pLysS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Standard plunger / Method: Blot about 2-3 seconds before plunging. |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG/ST |
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Date | Jan 1, 1999 |
Image recording | Category: 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 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 48600 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.1 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: side-entry / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Details | The number of classes analysed was 650. In the final reconstruction were used only 430. |
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CTF correction | Details: CTF correction of each particle |
Final reconstruction | Applied 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 |
Final two d classification | Number classes: 430 |
-Atomic model buiding 1
Software | Name: Molrep |
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Details | Protocol: Angular reconstitution |