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Yorodumi- PDB-6b23: Capsid protein and C-terminal part of CpmB protein in the Staphyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b23 | ||||||
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Title | Capsid protein and C-terminal part of CpmB protein in the Staphylococcus aureus pathogenicity island 1 80alpha-derived procapsid | ||||||
Components |
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Keywords | VIRUS / major capsid protein / HK97-like fold / scaffolding protein / procapsid | ||||||
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 Function and homology information | ||||||
Biological species | Staphylococcus phage 80alpha (virus) Staphylococcus aureus (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Kizziah, J.L. / Dearborn, A.D. / Dokland, T. | ||||||
Funding support | United States, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6b23.cif.gz | 256 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b23.ent.gz | 205.9 KB | Display | PDB format |
PDBx/mmJSON format | 6b23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6b23_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6b23_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6b23_validation.xml.gz | 43 KB | Display | |
Data in CIF | 6b23_validation.cif.gz | 66 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/6b23 ftp://data.pdbj.org/pub/pdb/validation_reports/b2/6b23 | HTTPS FTP |
-Related structure data
Related structure data | 7035MC 7030C 6b0xC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 36846.883 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus phage 80alpha (virus) / Gene: orf47 / Production host: Staphylococcus aureus (bacteria) / Strain (production host): RN4220 / References: UniProt: A4ZFB3 #2: Protein | Mass: 8281.234 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: ERS072840_02265 / Production host: Staphylococcus aureus (bacteria) / Strain (production host): ST63 / References: UniProt: O54465 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Lysogenic 80alpha with small terminase / Type: VIRUS Details: Lysogenic 80alpha with small terminase gene deletion Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 10.81 MDa / Experimental value: NO |
Source (natural) | Organism: Staphylococcus phage 80alpha (virus) |
Source (recombinant) | Organism: Staphylococcus aureus (bacteria) / Strain: RN4220 |
Details of virus | Empty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Staphylococcus aureus |
Virus shell | Name: Procapsid / Diameter: 546 nm / Triangulation number (T number): 7 |
Buffer solution | pH: 7.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) |
-Processing
Software | Name: REFMAC / Version: 5.8.0088 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING ONLY | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14087 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.7→3.7 Å / Cor.coef. Fo:Fc: 0.864 / SU B: 61.235 / SU ML: 0.676 / ESU R: 0.644 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 238.756 Å2
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Refinement step | Cycle: 1 / Total: 9854 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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