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Yorodumi- EMDB-6557: Cryo-EM of bacteriophage phi29 emptied particles treated by low p... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6557 | |||||||||
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Title | Cryo-EM of bacteriophage phi29 emptied particles treated by low pH without CsCl-gradient-purify | |||||||||
Map data | reconstruction of bacteriophage phi29 emptied particles treated by low pH and without CsCl-gradient-purified. | |||||||||
Sample |
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Keywords | bacteriophage phi29 / empty particles / tail knob protein gp9 | |||||||||
Biological species | Bacillus phage phi29 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 15.0 Å | |||||||||
Authors | Xu JW / Gui M / Wang DH / Xiang Y | |||||||||
Citation | Journal: Nature / Year: 2016 Title: The bacteriophage ϕ29 tail possesses a pore-forming loop for cell membrane penetration. Authors: Jingwei Xu / Miao Gui / Dianhong Wang / Ye Xiang / Abstract: Most bacteriophages are tailed bacteriophages with an isometric or a prolate head attached to a long contractile, long non-contractile, or short non-contractile tail. The tail is a complex machine ...Most bacteriophages are tailed bacteriophages with an isometric or a prolate head attached to a long contractile, long non-contractile, or short non-contractile tail. The tail is a complex machine that plays a central role in host cell recognition and attachment, cell wall and membrane penetration, and viral genome ejection. The mechanisms involved in the penetration of the inner host cell membrane by bacteriophage tails are not well understood. Here we describe structural and functional studies of the bacteriophage ϕ29 tail knob protein gene product 9 (gp9). The 2.0 Å crystal structure of gp9 shows that six gp9 molecules form a hexameric tube structure with six flexible hydrophobic loops blocking one end of the tube before DNA ejection. Sequence and structural analyses suggest that the loops in the tube could be membrane active. Further biochemical assays and electron microscopy structural analyses show that the six hydrophobic loops in the tube exit upon DNA ejection and form a channel that spans the lipid bilayer of the membrane and allows the release of the bacteriophage genomic DNA, suggesting that cell membrane penetration involves a pore-forming mechanism similar to that of certain non-enveloped eukaryotic viruses. A search of other phage tail proteins identified similar hydrophobic loops, which indicates that a common mechanism might be used for membrane penetration by prokaryotic viruses. These findings suggest that although prokaryotic and eukaryotic viruses use apparently very different mechanisms for infection, they have evolved similar mechanisms for breaching the cell membrane. | |||||||||
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_6557.map.gz | 59.2 MB | EMDB map data format | |
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Header (meta data) | emd-6557-v30.xml emd-6557.xml | 7.7 KB 7.7 KB | Display Display | EMDB header |
Images | 400_6557.gif 80_6557.gif | 30.1 KB 13.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6557 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6557 | HTTPS FTP |
-Validation report
Summary document | emd_6557_validation.pdf.gz | 78.4 KB | Display | EMDB validaton report |
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Full document | emd_6557_full_validation.pdf.gz | 77.4 KB | Display | |
Data in XML | emd_6557_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6557 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6557 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6557.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | reconstruction of bacteriophage phi29 emptied particles treated by low pH and without CsCl-gradient-purified. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.64 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : bacteriophage phi29 DNA emptied particles
Entire | Name: bacteriophage phi29 DNA emptied particles |
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Components |
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-Supramolecule #1000: bacteriophage phi29 DNA emptied particles
Supramolecule | Name: bacteriophage phi29 DNA emptied particles / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Bacillus phage phi29
Supramolecule | Name: Bacillus phage phi29 / type: virus / ID: 1 / Details: low pH treatment and DNA released / NCBI-ID: 10756 / Sci species name: Bacillus phage phi29 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Bacillus subtilis (bacteria) / synonym: BACTERIA(EUBACTERIA) |
Virus shell | Shell ID: 1 / Name: capsid protein, gp8 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 10mM MgCl2, 20mM NaCl, 10mM Tris-HCL |
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Grid | Details: Quantifoid, 2um x 2um, with thin carbon support |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | May 21, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 590 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particles |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 3420 |