+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28824 | |||||||||
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Title | Phi-29 expanded, DNA-packaged fiberless prohead | |||||||||
Map data | Phi-29 expanded, DNA-packaged fiberless prohead | |||||||||
Sample |
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Keywords | bacteriophage / prohead / HK97 fold / VIRUS | |||||||||
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 Function and homology information | |||||||||
Biological species | Bacillus phage phi29 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Woodson ME / Morais MC / Jardine PJ / Zhang W | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published 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 | emd_28824.map.gz | 887.1 MB | EMDB map data format | |
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Header (meta data) | emd-28824-v30.xml emd-28824.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28824_fsc.xml | 31 KB | Display | FSC data file |
Images | emd_28824.png | 217.2 KB | ||
Filedesc metadata | emd-28824.cif.gz | 6 KB | ||
Others | emd_28824_half_map_1.map.gz emd_28824_half_map_2.map.gz | 2.1 GB 2.1 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28824 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28824 | HTTPS FTP |
-Validation report
Summary document | emd_28824_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_28824_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_28824_validation.xml.gz | 38.2 KB | Display | |
Data in CIF | emd_28824_validation.cif.gz | 50.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28824 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28824 | HTTPS FTP |
-Related structure data
Related structure data | 8f2oMC 8f2mC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_28824.map.gz / Format: CCP4 / Size: 953.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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 |
-Sample components
-Entire : Bacillus phage phi29
Entire | Name: Bacillus phage phi29 (virus) |
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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: Bacillus subtilis (bacteria) |
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: Bacillus phage phi29 (virus) |
Molecular weight | Theoretical: 49.894906 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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 | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | TFS KRIOS |
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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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8f2o: |