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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Phi-29 expanded, DNA-packaged fiberless prohead | |||||||||
![]() | Phi-29 expanded, DNA-packaged fiberless prohead | |||||||||
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Function / homology | viral procapsid / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / T=3 icosahedral viral capsid / Major capsid protein![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Woodson ME / Morais MC / Jardine PJ / Zhang W | |||||||||
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 | ![]() | 887.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.7 KB 17.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 31 KB | Display | ![]() |
Images | ![]() | 217.2 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Others | ![]() ![]() | 2.1 GB 2.1 GB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8f2oMC ![]() 8f2mC M: atomic model generated by this map 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 | Phi-29 expanded, DNA-packaged fiberless prohead | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half 1
File | emd_28824_half_map_1.map | ||||||||||||
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Annotation | half 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half 2
File | emd_28824_half_map_2.map | ||||||||||||
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Annotation | half 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: Major capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 47 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 49.894906 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MRITFNDVKT SLGITESYDI VNAIRNSQGD NFKSYVPLAT ANNVAEVGAG ILINQTVQND FITSLVDRIG LVVIRQVSLN NPLKKFKKG QIPLGRTIEE IYTDITKEKQ YDAEEAEQKV FEREMPNVKT LFHERNRQGF YHQTIQDDSL KTAFVSWGNF E SFVSSIIN ...String: MRITFNDVKT SLGITESYDI VNAIRNSQGD NFKSYVPLAT ANNVAEVGAG ILINQTVQND FITSLVDRIG LVVIRQVSLN NPLKKFKKG QIPLGRTIEE IYTDITKEKQ YDAEEAEQKV FEREMPNVKT LFHERNRQGF YHQTIQDDSL KTAFVSWGNF E SFVSSIIN AIYNSAEVDE YEYMKLLVDN YYSKGLFTTV KIDEPTSSTG ALTEFVKKMR ATARKLTLPQ GSRDWNSMAV RT RSYMEDL HLIIDADLEA ELDVDVLAKA FNMNRTDFLG NVTVIDGFAS TGLEAVLVDK DWFMVYDNLH KMETVRNPRG LYW NYYYHV WQTLSVSRFA NAVAFVSGDV PAVTQVIVSP NIAAVKQGGQ QQFTAYVRAT NAKDHKVVWS VEGGSTGTAI TGDG LLSVS GNEDNQLTVK ATVDIGTEDK PKLVVGEAVV SIRPNNASGG AQA UniProtKB: Major capsid protein |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.8 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: OTHER | ||||||||||||
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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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 5593 / Average electron dose: 35.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-8f2o: |