+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28822 | |||||||||
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Title | Phi-29 scaffolding protein bound to intermediate-state MCP | |||||||||
Map data | Phi-29 scaffolding protein bound to intermediate-state MCP | |||||||||
Sample |
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Keywords | bacteriophage / prohead / scaffold / HK97 fold / VIRUS | |||||||||
Function / homology | Function and homology information viral scaffold / viral procapsid / T=3 icosahedral viral capsid / virion assembly / DNA binding Similarity search - Function | |||||||||
Biological species | Bacillus phage phi29 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Woodson ME / Morais MC / Jardine PJ / Scott SD | |||||||||
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_28822.map.gz | 26.1 MB | EMDB map data format | |
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Header (meta data) | emd-28822-v30.xml emd-28822.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28822_fsc.xml | 7.7 KB | Display | FSC data file |
Images | emd_28822.png | 182.2 KB | ||
Filedesc metadata | emd-28822.cif.gz | 6.1 KB | ||
Others | emd_28822_half_map_1.map.gz emd_28822_half_map_2.map.gz | 29.4 MB 29.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28822 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28822 | HTTPS FTP |
-Validation report
Summary document | emd_28822_validation.pdf.gz | 862.4 KB | Display | EMDB validaton report |
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Full document | emd_28822_full_validation.pdf.gz | 862 KB | Display | |
Data in XML | emd_28822_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | emd_28822_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28822 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28822 | HTTPS FTP |
-Related structure data
Related structure data | 8f2mMC 8f2oC C: citing same article (ref.) M: atomic model generated by this map |
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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_28822.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Phi-29 scaffolding protein bound to intermediate-state MCP | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.092 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_28822_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_28822_half_map_2.map | ||||||||||||
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Annotation | Half Map 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: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus phage phi29 (virus) |
Molecular weight | Theoretical: 49.894906 KDa |
Recombinant expression | Organism: Escherichia phage EcSzw-2 (virus) |
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 |
-Macromolecule #2: Capsid assembly scaffolding protein
Macromolecule | Name: Capsid assembly scaffolding protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus phage phi29 (virus) |
Molecular weight | Theoretical: 11.282529 KDa |
Recombinant expression | Organism: Escherichia phage EcSzw-2 (virus) |
Sequence | String: MPLKPEEHED ILNKLLDPEL AQSERTEALQ QLRVNYGSFV SEYNDLTKSH EKLAAEKDDL IVSNSKLFRQ IGLTDKQEED HKKADISET ITIEDLEAK UniProtKB: Capsid assembly scaffolding 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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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-8f2m: |