+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5445 | |||||||||
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Title | Icosahedral reconstruction of the Streptococcus phage C1 capsid | |||||||||
Map data | icosahedral reconstruction of phage C1 capsid | |||||||||
Sample |
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Keywords | bacteriophage / capsid / HK97 fold / Podoviridae | |||||||||
Biological species | Streptococcus phage C1 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.3 Å | |||||||||
Authors | Aksyuk AA / Bowman VD / Kaufmann B / Fields C / Klose T / Holdaway HA / Fischetti VA / Rossmann MG | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2012 Title: Structural investigations of a Podoviridae streptococcus phage C1, implications for the mechanism of viral entry. Authors: Anastasia A Aksyuk / Valorie D Bowman / Bärbel Kaufmann / Christopher Fields / Thomas Klose / Heather A Holdaway / Vincent A Fischetti / Michael G Rossmann / Abstract: The Podoviridae phage C1 was one of the earliest isolated bacteriophages and the first virus documented to be active against streptococci. The icosahedral and asymmetric reconstructions of the virus ...The Podoviridae phage C1 was one of the earliest isolated bacteriophages and the first virus documented to be active against streptococci. The icosahedral and asymmetric reconstructions of the virus were calculated using cryo-electron microscopy. The capsid protein has an HK97 fold arranged into a T = 4 icosahedral lattice. The C1 tail is terminated with a ϕ29-like knob, surrounded by a skirt of twelve long appendages with novel morphology. Several C1 structural proteins have been identified, including a candidate for an appendage. The crystal structure of the knob has an N-terminal domain with a fold observed previously in tube forming proteins of Siphoviridae and Myoviridae phages. The structure of C1 suggests the mechanisms by which the virus digests the cell wall and ejects its genome. Although there is little sequence similarity to other phages, conservation of the structural proteins demonstrates a common origin of the head and tail, but more recent evolution of the appendages. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5445.map.gz | 558.4 MB | EMDB map data format | |
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Header (meta data) | emd-5445-v30.xml emd-5445.xml | 7.5 KB 7.5 KB | Display Display | EMDB header |
Images | emd_5445_1.jpg | 99.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5445 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5445 | HTTPS FTP |
-Validation report
Summary document | emd_5445_validation.pdf.gz | 77.6 KB | Display | EMDB validaton report |
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Full document | emd_5445_full_validation.pdf.gz | 76.7 KB | Display | |
Data in XML | emd_5445_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5445 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5445 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5445.map.gz / Format: CCP4 / Size: 586.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | icosahedral reconstruction of phage C1 capsid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : C1 capsid
Entire | Name: C1 capsid |
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Components |
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-Supramolecule #1000: C1 capsid
Supramolecule | Name: C1 capsid / type: sample / ID: 1000 / Oligomeric state: T=4 capsid / Number unique components: 1 |
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-Supramolecule #1: Streptococcus phage C1
Supramolecule | Name: Streptococcus phage C1 / type: virus / ID: 1 / NCBI-ID: 230871 / Sci species name: Streptococcus phage C1 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Streptococcus (bacteria) / synonym: BACTERIA(EUBACTERIA) |
Virus shell | Shell ID: 1 / Name: C1 / Diameter: 500 Å / T number (triangulation number): 4 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
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-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | May 1, 2011 |
Image recording | Digitization - Scanner: NIKON COOLSCAN |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 8.3 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 17000 |
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