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- EMDB-1260: Structural changes of bacteriophage phi29 upon DNA packaging and ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1260 | |||||||||
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Title | Structural changes of bacteriophage phi29 upon DNA packaging and release. | |||||||||
![]() | Bacteriophage phi29 emptied head. Five fold symmetry was used in the reconstruction | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 20.0 Å | |||||||||
![]() | Xiang Y / Morais MC / Battisti AJ / Grimes S / Jardine PJ / Anderson DL / Rossmann MG | |||||||||
![]() | ![]() Title: Structural changes of bacteriophage phi29 upon DNA packaging and release. Authors: Ye Xiang / Marc C Morais / Anthony J Battisti / Shelley Grimes / Paul J Jardine / Dwight L Anderson / Michael G Rossmann / ![]() Abstract: Cryo-electron microscopy three-dimensional reconstructions have been made of mature and of emptied bacteriophage phi29 particles without making symmetry assumptions. Comparisons of these structures ...Cryo-electron microscopy three-dimensional reconstructions have been made of mature and of emptied bacteriophage phi29 particles without making symmetry assumptions. Comparisons of these structures with each other and with the phi29 prohead indicate how conformational changes might initiate successive steps of assembly and infection. The 12 adsorption capable 'appendages' were found to have a structure homologous to the bacteriophage P22 tailspikes. Two of the appendages are extended radially outwards, away from the long axis of the virus, whereas the others are around and parallel to the phage axis. The appendage orientations are correlated with the symmetry-mismatched positions of the five-fold related head fibers, suggesting a mechanism for partial cell wall digestion upon rotation of the head about the tail when initiating infection. The narrow end of the head-tail connector is expanded in the mature virus. Gene product 3, bound to the 5' ends of the genome, appears to be positioned within the expanded connector, which may potentiate the release of DNA-packaging machine components, creating a binding site for attachment of the tail. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 12.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.2 KB 8.2 KB | Display Display | ![]() |
Images | ![]() | 24.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 261.5 KB | Display | ![]() |
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Full document | ![]() | 260.6 KB | Display | |
Data in XML | ![]() | 6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Bacteriophage phi29 emptied head. Five fold symmetry was used in the reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : emptied bacteriophage phi29
Entire | Name: emptied bacteriophage phi29 |
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Components |
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-Supramolecule #1000: emptied bacteriophage phi29
Supramolecule | Name: emptied bacteriophage phi29 / 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: empty phi29 / NCBI-ID: 10756 / Sci species name: Bacillus phage phi29 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: Yes |
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Host (natural) | Organism: ![]() ![]() |
Virus shell | Shell ID: 1 / Name: prolate icosahedron / Diameter: 530 Å / T number (triangulation number): 3 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 / Details: 20mM NaCl, 10mM Tris-HCL,1mM MgCl2 |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
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Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/T |
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Date | Dec 12, 2008 |
Image recording | Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 65 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: 12 / Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
CTF correction | Details: Phase flip |
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Final reconstruction | Applied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 6193 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: EMFIT |
Refinement | Space: REAL |