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- PDB-8eb7: Cryo-EM structure of the in-situ gp4-gp10-gp9N from bacteriophage P22 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8eb7 | ||||||
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Title | Cryo-EM structure of the in-situ gp4-gp10-gp9N from bacteriophage P22 | ||||||
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![]() | VIRAL PROTEIN / Bacteriophage P22 | ||||||
Function / homology | ![]() endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / symbiont entry into host cell via disruption of host cell wall peptidoglycan / symbiont genome ejection through host cell envelope, short tail mechanism / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / adhesion receptor-mediated virion attachment to host cell ...endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / symbiont entry into host cell via disruption of host cell wall peptidoglycan / symbiont genome ejection through host cell envelope, short tail mechanism / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / adhesion receptor-mediated virion attachment to host cell / hydrolase activity / virion attachment to host cell Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
![]() | Wang, C. / Liu, J. / Molineux, I.J. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 909.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 147.4 KB | Display | |
Data in CIF | ![]() | 235.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 27793MC ![]() 8eapC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 12126.580 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P12528, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #2: Protein | Mass: 16359.296 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 52410.852 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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 |
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Sample preparation
Component | Name: Cryo-EM structure of the in-situ gp4-gp10-gp9N from bacteriophage P22 Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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) |
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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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32650 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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