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- PDB-8bcp: Cryo-EM structure of the proximal end of bacteriophage T5 tail : ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bcp | |||||||||
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Title | Cryo-EM structure of the proximal end of bacteriophage T5 tail : p142 tail terminator protein hexamer and pb6 tail tube protein trimer | |||||||||
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![]() | VIRAL PROTEIN / Bacteriophage / Siphophage / T5 / tail terminator / Trp | |||||||||
Function / homology | ![]() virus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / viral release from host cell by cytolysis Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.88 Å | |||||||||
![]() | Linares, R. / Effantin, G. / Breyton, C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of the proximal end of bacteriophage T5 tail, in its native state and after interaction with its bacterial receptor Authors: Linares, R. / Effantin, G. / Breyton, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 395.4 KB | Display | ![]() |
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PDB format | ![]() | 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 | ![]() | 69.2 KB | Display | |
Data in CIF | ![]() | 104.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 15967MC ![]() 8bcuC 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: 18378.643 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 50459.215 Da / Num. of mol.: 3 / 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: Escherichia virus T5 / Type: VIRUS Details: Pure T5 tails obtained by infecting E. coli F strain with the amber mutant phage T5D20am30d Entity ID: all / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE | |||||||||||||||||||||||||
Natural host | Organism: Escherichia coli / Strain: F | |||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Pure T5 tails obtained by infecting E. coli F strain with the amber mutant phage T5D20am30d | |||||||||||||||||||||||||
Specimen support | Details: 25 mA / Grid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K Details: 3 uL of T5 tails sample were deposited on a freshly glow discharged EM grid and plunge-frozen in nitrogen-cooled liquid ethane using a ThermoFisher Mark IV Vitrobot device (100 percent ...Details: 3 uL of T5 tails sample were deposited on a freshly glow discharged EM grid and plunge-frozen in nitrogen-cooled liquid ethane using a ThermoFisher Mark IV Vitrobot device (100 percent humidity, 20 Celsius degrees, 5 s blotting time, blot force 0) |
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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 magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 |
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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 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9952 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | B value: 146 / Protocol: BACKBONE TRACE / Space: REAL | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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