+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7030 | |||||||||
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Title | Staphylococcus aureus phage 80alpha procapsid | |||||||||
Map data | Capsid protein and C-terminal part of scaffolding protein in the Staphylococcus aureus phage 80alpha procapsid: clipped map used for model building and refinement in Coot and REFMAC | |||||||||
Sample |
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Keywords | major capsid protein / HK97-like fold / scaffolding protein / procapsid / VIRUS | |||||||||
Function / homology | Protein of unknown function DUF4355 / Domain of unknown function (DUF4355) / viral scaffold / Phage capsid / Phage capsid family / viral capsid / Scaffold protein / Major capsid protein Function and homology information | |||||||||
Biological species | Staphylococcus phage 80alpha (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Kizziah JL / Dearborn AD | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Elife / Year: 2017 Title: Competing scaffolding proteins determine capsid size during mobilization of pathogenicity islands. Authors: Altaira D Dearborn / Erin A Wall / James L Kizziah / Laura Klenow / Laura K Parker / Keith A Manning / Michael S Spilman / John M Spear / Gail E Christie / Terje Dokland / Abstract: pathogenicity islands (SaPIs), such as SaPI1, exploit specific helper bacteriophages, like 80α, for their high frequency mobilization, a process termed 'molecular piracy'. SaPI1 redirects the ... pathogenicity islands (SaPIs), such as SaPI1, exploit specific helper bacteriophages, like 80α, for their high frequency mobilization, a process termed 'molecular piracy'. SaPI1 redirects the helper's assembly pathway to form small capsids that can only accommodate the smaller SaPI1 genome, but not a complete phage genome. SaPI1 encodes two proteins, CpmA and CpmB, that are responsible for this size redirection. We have determined the structures of the 80α and SaPI1 procapsids to near-atomic resolution by cryo-electron microscopy, and show that CpmB competes with the 80α scaffolding protein (SP) for a binding site on the capsid protein (CP), and works by altering the angle between capsomers. We probed these interactions genetically and identified second-site suppressors of lethal mutations in SP. Our structures show, for the first time, the detailed interactions between SP and CP in a bacteriophage, providing unique insights into macromolecular assembly processes. | |||||||||
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_7030.map.gz | 199.6 MB | EMDB map data format | |
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Header (meta data) | emd-7030-v30.xml emd-7030.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7030_fsc.xml | 26.6 KB | Display | FSC data file |
Images | emd_7030.png | 300.2 KB | ||
Filedesc metadata | emd-7030.cif.gz | 5.6 KB | ||
Others | emd_7030_additional.map.gz | 974.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7030 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7030 | HTTPS FTP |
-Validation report
Summary document | emd_7030_validation.pdf.gz | 582.2 KB | Display | EMDB validaton report |
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Full document | emd_7030_full_validation.pdf.gz | 581.8 KB | Display | |
Data in XML | emd_7030_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | emd_7030_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7030 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7030 | HTTPS FTP |
-Related structure data
Related structure data | 6b0xMC 7035C 6b23C 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_7030.map.gz / Format: CCP4 / Size: 210.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Capsid protein and C-terminal part of scaffolding protein in the Staphylococcus aureus phage 80alpha procapsid: clipped map used for model building and refinement in Coot and REFMAC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Capsid protein and C-terminal part of scaffolding protein...
File | emd_7030_additional.map | ||||||||||||
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Annotation | Capsid protein and C-terminal part of scaffolding protein in the Staphylococcus aureus phage 80alpha procapsid: final map sharpened with a B-factor of 300 to 6 Angstrom resolution (cutoff at 3 Angstrom) | ||||||||||||
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 Details: Lysogenic 80alpha with small terminase gene deletion 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: 25.27 MDa |
Virus shell | Shell ID: 1 / Name: Procapsid / Diameter: 546.0 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 phage 80alpha (virus) |
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 |
-Macromolecule #2: Scaffold protein
Macromolecule | Name: Scaffold protein / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus phage 80alpha (virus) |
Molecular weight | Theoretical: 23.410941 KDa |
Recombinant expression | Organism: Staphylococcus aureus (bacteria) |
Sequence | String: MEENKLKFNL QFFADQSDDP DEPGGDGKKG NPDKKENDEG TEITFTPEQQ KKVDEILERR VAHEKKKADE YAKEKAAEAA KEAAKLAKM NKDQKDEYER EQMEKELEQL RSEKQLNEMR SEARKMLSEA EVDSSDEVVN LVVTDTAEQT KSNVEAFSNA V KKAVNEAV ...String: MEENKLKFNL QFFADQSDDP DEPGGDGKKG NPDKKENDEG TEITFTPEQQ KKVDEILERR VAHEKKKADE YAKEKAAEAA KEAAKLAKM NKDQKDEYER EQMEKELEQL RSEKQLNEMR SEARKMLSEA EVDSSDEVVN LVVTDTAEQT KSNVEAFSNA V KKAVNEAV KVNARQSPLT GGDSFNHSTK NKPQNLAEIA RQKRIIKN UniProtKB: Scaffold 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 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |