+Open data
-Basic information
Entry | Database: PDB / ID: 8f2m | ||||||
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Title | Phi-29 scaffolding protein bound to intermediate-state MCP | ||||||
Components |
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Keywords | VIRUS / bacteriophage / prohead / scaffold / HK97 fold | ||||||
Function / homology | Function and homology information viral scaffold / viral procapsid / T=3 icosahedral viral capsid / virion assembly / DNA binding Similarity search - Function | ||||||
Biological species | Bacillus phage phi29 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Woodson, M.E. / Morais, M.C. / Jardine, P.J. / Scott, S.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Scaffold Oligomers Control Prohead Expansion Authors: Woodson, M.E. / Morais, M.C. / Prokhorov, N.S. / Scott, S.D. / Zhang, W. / Choi, K.H. / Jardine, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f2m.cif.gz | 117.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f2m.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 8f2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/8f2m ftp://data.pdbj.org/pub/pdb/validation_reports/f2/8f2m | HTTPS FTP |
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-Related structure data
Related structure data | 28822MC 8f2oC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 49894.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage phi29 (virus) / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: P13849 |
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#2: Protein | Mass: 11282.529 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage phi29 (virus) / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: P13848 |
-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: Bacillus phage phi29Bacillus virus phi29 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Bacillus phage phi29 (virus) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||
Details of virus | Empty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE | ||||||||||||||||||||
Natural host | Organism: Bacillus subtilis | ||||||||||||||||||||
Virus shell | Name: capsid / Diameter: 35 nm / Triangulation number (T number): 3 | ||||||||||||||||||||
Buffer solution | pH: 7.8 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 35 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5593 |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 89000 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53000 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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