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- EMDB-28821: bacteriophage phi-29 MCP gp-8 penton in intermediate maturation s... -
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Open data
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Basic information
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Title | bacteriophage phi-29 MCP gp-8 penton in intermediate maturation state, with associated scaffold gp7 dimer | |||||||||
![]() | bacteriophage phi-29 MCP gp-8 penton in intermediate maturation state, with associated scaffold gp7 dimer | |||||||||
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![]() | bacteriophage / prohead / HK97 fold / VIRUS | |||||||||
Function / homology | ![]() viral scaffold / viral procapsid / T=3 icosahedral viral capsid / virion assembly / DNA binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Woodson ME / Morais MC / Prokhorov NS / Zhang W / Jardine PJ | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Scaffold Oligomers Control Prohead Expansion Authors: Woodson ME / Morais MC / Prokhorov NS / Scott SD / Zhang W / Choi KH / Jardine PJ | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 16.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.5 KB 17.5 KB | Display Display | ![]() |
Images | ![]() | 136.7 KB | ||
Filedesc metadata | ![]() | 5.1 KB | ||
Others | ![]() ![]() | 16.7 MB 16.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 795.6 KB | Display | ![]() |
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Full document | ![]() | 795.2 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 11.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8f2mC ![]() 8f2oC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | bacteriophage phi-29 MCP gp-8 penton in intermediate maturation state, with associated scaffold gp7 dimer | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.272 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half Map 1
File | emd_28821_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_28821_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Bacillus phage phi29
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1: Bacillus phage phi29
Supramolecule | Name: Bacillus phage phi29 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2884424 / Sci species name: Bacillus phage phi29 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: ![]() ![]() |
Virus shell | Shell ID: 1 / Name: capsid / Diameter: 35.0 Å / T number (triangulation number): 3 |
-Macromolecule #1: bacteriophage phi-29 MCP gp8
Macromolecule | Name: bacteriophage phi-29 MCP gp8 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Sequence | String: MRITFNDVKT SLGITESYDI VNAIRNSQGD NFKSYVPLAT ANNVAEVGAG ILINQTVQND FITSLVDRI GLVVIRQVSL NNPLKKFKKG QIPLGRTIEE IYTDITKEKQ YDAEEAEQKV F EREMPNVK TLFHERNRQG FYHQTIQDDS LKTAFVSWGN FESFVSSIIN ...String: MRITFNDVKT SLGITESYDI VNAIRNSQGD NFKSYVPLAT ANNVAEVGAG ILINQTVQND FITSLVDRI GLVVIRQVSL NNPLKKFKKG QIPLGRTIEE IYTDITKEKQ YDAEEAEQKV F EREMPNVK TLFHERNRQG FYHQTIQDDS LKTAFVSWGN FESFVSSIIN AIYNSAEVDE YE YMKLLVD NYYSKGLFTT VKIDEPTSST GALTEFVKKM RATARKLTLP QGSRDWNSMA VRT RSYMED LHLIIDADLE AELDVDVLAK AFNMNRTDFL GNVTVIDGFA STGLEAVLVD KDWF MVYDN LHKMETVRNP RGLYWNYYYH VWQTLSVSRF ANAVAFVSGD VPAVTQVIVS PNIAA VKQG GQQQFTAYVR ATNAKDHKVV WSVEGGSTGT AITGDGLLSV SGNEDNQLTV KATVDI GTE DKPKLVVGEA VVSIRPNNAS GGAQA UniProtKB: Major capsid protein |
-Macromolecule #2: bacteriophage phi-29 scaffold protein gp7
Macromolecule | Name: bacteriophage phi-29 scaffold protein gp7 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Sequence | String: MPLKPEEHED ILNKLLDPEL AQSERTEALQ QLRVNYGSFV SEYNDLTKSH EKLAAEKDDL IVSNSKLFR QIGLTDKQEE DHKKADISET ITIEDLEAK UniProtKB: Capsid assembly scaffolding protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 2730 / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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