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- EMDB-7035: Staphylococcus aureus pathogenicity island 1 80alpha-derived procapsid -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7035 | |||||||||
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Title | Staphylococcus aureus pathogenicity island 1 80alpha-derived procapsid | |||||||||
![]() | Capsid protein and C-terminal part of CpmB protein in the Staphylococcus aureus pathogenicity island 1 80alpha-derived procapsid: clipped map used for model building and refinement in Coot and REFMAC. | |||||||||
![]() | Lysogenic 80alpha with small terminase != Staphylococcus phage 80alpha Lysogenic 80alpha with small terminase
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![]() | major capsid protein / HK97-like fold / scaffolding protein / procapsid / VIRUS | |||||||||
Function / homology | Pathogenicity island protein gp6, Staphylococcus / Pathogenicity island protein gp6 superfamily / Pathogenicity island protein gp6 in Staphylococcus / Phage capsid / Phage capsid family / viral capsid / Major capsid protein / Hypothetical mobile element-associated protein![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Kizziah JL / Dearborn AD | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 160.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14 KB 14 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 21 KB | Display | ![]() |
Images | ![]() | 288.1 KB | ||
Filedesc metadata | ![]() | 5.5 KB | ||
Others | ![]() | 480.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6b23MC ![]() 7030C ![]() 6b0xC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Capsid protein and C-terminal part of CpmB protein in the Staphylococcus aureus pathogenicity island 1 80alpha-derived procapsid: clipped map used for model building and refinement in Coot and REFMAC. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.212 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 CpmB protein...
File | emd_7035_additional.map | ||||||||||||
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Annotation | Capsid protein and C-terminal part of CpmB protein in the Staphylococcus aureus pathogenicity island 1 80alpha-derived procapsid: final map from reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Lysogenic 80alpha with small terminase
Entire | Name: Lysogenic 80alpha with small terminase |
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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: ![]() ![]() |
Molecular weight | Theoretical: 10.81 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: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 36.846883 KDa |
Recombinant expression | Organism: ![]() ![]() |
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: Capsid morphogenesis B protein
Macromolecule | Name: Capsid morphogenesis B protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 8.281234 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: METKYELNNT KKVANAFGLN EEDTNLLINA VDLDIKNNMQ EISSELQQSE QSKQKQYGTT LQNLAKQNRI IK UniProtKB: Hypothetical mobile element-associated protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |