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Yorodumi- PDB-8eao: Cryo-EM structure of the in-situ gp1-gp4 complex from bacteriopha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8eao | ||||||
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Title | Cryo-EM structure of the in-situ gp1-gp4 complex from bacteriophage P22 | ||||||
Components |
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Keywords | VIRAL PROTEIN / Bacteriophage P22 | ||||||
Function / homology | Function and homology information viral DNA genome packaging, headful / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / viral DNA genome packaging / virus tail / virion assembly / hydrolase activity Similarity search - Function | ||||||
Biological species | Salmonella phage P22 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Wang, C. / Liu, J. / Molineux, I.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: In-situ structure of tail machine reveals mechanistic insights into P22 assembly. Authors: Wang, C. / Liu, J. / Molineux, I.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eao.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8eao.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 8eao.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8eao_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8eao_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8eao_validation.xml.gz | 217.5 KB | Display | |
Data in CIF | 8eao_validation.cif.gz | 339.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/8eao ftp://data.pdbj.org/pub/pdb/validation_reports/ea/8eao | HTTPS FTP |
-Related structure data
Related structure data | 27792MC 8eanC 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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1 |
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-Components
#1: Protein | Mass: 16231.166 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Salmonella phage P22 (virus) / References: UniProt: P26746 #2: Protein | Mass: 71116.539 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Salmonella phage P22 (virus) / References: UniProt: P26744 |
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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: Cryo-EM structure of the in-situ gp1-gp4 complex from bacteriophgage P22 Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Salmonella phage P22 (virus) |
Buffer solution | pH: 7.5 |
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 / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73420 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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