+Open data
-Basic information
Entry | Database: PDB / ID: 8giu | ||||||
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Title | Mycobacterium phage Patience | ||||||
Components |
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Keywords | VIRUS / HK97-fold / T=7 / tailed bacteriophage | ||||||
Function / homology | Uncharacterized protein / Uncharacterized protein / Capsid protein Function and homology information | ||||||
Biological species | Mycobacterium phage Patience (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.39 Å | ||||||
Authors | Podgorski, J.M. / White, S.J. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: A novel accessory protein stabilizes the capsid of two actinobacteriophages Authors: Podgorski, J.M. / Porgorski, J. / Gosselin, S. / Abad, L. / Jacobs-Sera, D. / Brown, C. / Hatfull, G. / Gogarten, P. / Luque, A. / White, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8giu.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8giu.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 8giu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8giu_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8giu_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8giu_validation.xml.gz | 122.4 KB | Display | |
Data in CIF | 8giu_validation.cif.gz | 187.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/8giu ftp://data.pdbj.org/pub/pdb/validation_reports/gi/8giu | HTTPS FTP |
-Related structure data
Related structure data | 40077MC 8sajC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 10549.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Patience (virus) / References: UniProt: G1JWB5 #2: Protein | Mass: 43845.391 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Patience (virus) / References: UniProt: G1JWD4 #3: Protein | Mass: 23845.107 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Patience (virus) / References: UniProt: G1JWD3 |
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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: Mycobacterium phage Patience / Type: VIRUS / Entity ID: all / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Mycobacterium phage Patience (virus) | ||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION | ||||||||||||||||||||
Natural host | Organism: Mycolicibacterium smegmatis MC2 155 | ||||||||||||||||||||
Virus shell | Diameter: 760 nm / Triangulation number (T number): 7 | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 10 mg/ml / 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: 283 K |
-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 / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 8640 |
-Processing
EM software |
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CTF correction | Details: Standard CTF correction inside RELION's reconstruction. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61957 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL Details: Amino acid sequence built into the map for a single major capsid protein and refined with Phenix. Model then used for rest of asymmetric unit and refined with Phenix. Final step involved using Isolde. |