+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7332 | |||||||||
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Title | Staphylococcus aureus phage 80alpha mature capsid | |||||||||
Map data | Staphylococcus aureus phage 80alpha mature capsid. Clipped and sharpened map used for model building and refinement. Sharpened using bsoft by applying B factor of -800 up to 8 Angstrom resolution (map set to zero at higher than 4 Angstrom). | |||||||||
Sample |
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Keywords | major capsid protein / HK97-like fold / mature capsid / VIRUS | |||||||||
Function / homology | Phage capsid / Phage capsid family / viral capsid / Major capsid protein Function and homology information | |||||||||
Biological species | Staphylococcus virus 80alpha / Staphylococcus phage 80alpha (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.2 Å | |||||||||
Authors | Dokland T | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Viruses / Year: 2017 Title: Cleavage and Structural Transitions during Maturation of Staphylococcus aureus Bacteriophage 80α and SaPI1 Capsids. Authors: James L Kizziah / Keith A Manning / Altaira D Dearborn / Erin A Wall / Laura Klenow / Rosanne L L Hill / Michael S Spilman / Scott M Stagg / Gail E Christie / Terje Dokland / Abstract: In the tailed bacteriophages, DNA is packaged into spherical procapsids, leading to expansion into angular, thin-walled mature capsids. In many cases, this maturation is accompanied by cleavage of ...In the tailed bacteriophages, DNA is packaged into spherical procapsids, leading to expansion into angular, thin-walled mature capsids. In many cases, this maturation is accompanied by cleavage of the major capsid protein (CP) and other capsid-associated proteins, including the scaffolding protein (SP) that serves as a chaperone for the assembly process. bacteriophage 80α is capable of high frequency mobilization of mobile genetic elements called pathogenicity islands (SaPIs), such as SaPI1. SaPI1 redirects the assembly pathway of 80α to form capsids that are smaller than those normally made by the phage alone. Both CP and SP of 80α are N-terminally processed by a host-encoded protease, Prp. We have analyzed phage mutants that express pre-cleaved or uncleavable versions of CP or SP, and show that the N-terminal sequence in SP is absolutely required for assembly, but does not need to be cleaved in order to produce viable capsids. Mutants with pre-cleaved or uncleavable CP display normal viability. We have used cryo-EM to solve the structures of mature capsids from an 80α mutant expressing uncleavable CP, and from wildtype SaPI1. Comparisons with structures of 80α and SaPI1 procapsids show that capsid maturation involves major conformational changes in CP, consistent with a release of the CP N-arm by SP. The hexamers reorganize during maturation to accommodate the different environments in the 80α and SaPI1 capsids. | |||||||||
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_7332.map.gz | 396.6 MB | EMDB map data format | |
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Header (meta data) | emd-7332-v30.xml emd-7332.xml | 14 KB 14 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7332_fsc.xml | 26.2 KB | Display | FSC data file |
Images | emd_7332.png | 273 KB | ||
Filedesc metadata | emd-7332.cif.gz | 5.7 KB | ||
Others | emd_7332_additional.map.gz | 117.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7332 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7332 | HTTPS FTP |
-Validation report
Summary document | emd_7332_validation.pdf.gz | 642.6 KB | Display | EMDB validaton report |
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Full document | emd_7332_full_validation.pdf.gz | 642.2 KB | Display | |
Data in XML | emd_7332_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_7332_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7332 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7332 | HTTPS FTP |
-Related structure data
Related structure data | 6c21MC 7333C 6c22C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7332.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Staphylococcus aureus phage 80alpha mature capsid. Clipped and sharpened map used for model building and refinement. Sharpened using bsoft by applying B factor of -800 up to 8 Angstrom resolution (map set to zero at higher than 4 Angstrom). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Staphylococcus aureus phage 80alpha mature capsid. Unclipped and...
File | emd_7332_additional.map | ||||||||||||
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Annotation | Staphylococcus aureus phage 80alpha mature capsid. Unclipped and unsharpened version of map used for model building and refinement. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Staphylococcus phage 80alpha
Entire | Name: Staphylococcus phage 80alpha (virus) |
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Components |
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-Supramolecule #1: Staphylococcus phage 80alpha
Supramolecule | Name: Staphylococcus phage 80alpha / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 53369 / Sci species name: Staphylococcus phage 80alpha / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Staphylococcus aureus (bacteria) |
Molecular weight | Theoretical: 15.46 MDa |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 630.0 Å / T number (triangulation number): 7 |
-Macromolecule #1: Major head protein
Macromolecule | Name: Major head protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus virus 80alpha |
Molecular weight | Theoretical: 36.846883 KDa |
Recombinant expression | Organism: Staphylococcus aureus (bacteria) |
Sequence | String: MEQTQKLKLN LQHFASNNVK PQVFNPDNVM MHEKKDGTLM NEFTTPILQE VMENSKIMQL GKYEPMEGTE KKFTFWADKP GAYWVGEGQ KIETSKATWV NATMRAFKLG VILPVTKEFL NYTYSQFFEE MKPMIAEAFY KKFDEAGILN QGNNPFGKSI A QSIEKTNK ...String: MEQTQKLKLN LQHFASNNVK PQVFNPDNVM MHEKKDGTLM NEFTTPILQE VMENSKIMQL GKYEPMEGTE KKFTFWADKP GAYWVGEGQ KIETSKATWV NATMRAFKLG VILPVTKEFL NYTYSQFFEE MKPMIAEAFY KKFDEAGILN QGNNPFGKSI A QSIEKTNK VIKGDFTQDN IIDLEALLED DELEANAFIS KTQNRSLLRK IVDPETKERI YDRNSDSLDG LPVVNLKSSN LK RGELITG DFDKLIYGIP QLIEYKIDET AQLSTVKNED GTPVNLFEQD MVALRATMHV ALHIADDKAF AKLVPADKRT DSV PGEV 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: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 15.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 96000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-6c21: |