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Yorodumi- PDB-2bsg: The modeled structure of fibritin (gpwac) of bacteriophage T4 bas... -
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-Basic information
Entry | Database: PDB / ID: 2bsg | ||||||
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Title | The modeled structure of fibritin (gpwac) of bacteriophage T4 based on cryo-EM reconstruction of the extended tail of bacteriophage T4 | ||||||
Components | FIBRITIN | ||||||
Keywords | VIRAL PROTEIN / ATTACHMENT PROTEIN / BACTERIOPHAGE ASSEMBLY / BACTERIOPHAGE T4 / CHAPERONE / FIBRITIN / STRUCTURAL PROTEIN | ||||||
Function / homology | Fibritin C-terminal / Fibritin C-terminal region / virion component / Fibritin Function and homology information | ||||||
Biological species | BACTERIOPHAGE T4 (virus) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 15 Å | ||||||
Model type details | CA ATOMS ONLY, CHAIN A, B, C | ||||||
Authors | Kostyuchenko, V.A. / Chipman, P.R. / Leiman, P.G. / Arisaka, F. / Mesyanzhinov, V.V. / Rossmann, M.G. | ||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2005 Title: The tail structure of bacteriophage T4 and its mechanism of contraction. Authors: Victor A Kostyuchenko / Paul R Chipman / Petr G Leiman / Fumio Arisaka / Vadim V Mesyanzhinov / Michael G Rossmann / Abstract: Bacteriophage T4 and related viruses have a contractile tail that serves as an efficient mechanical device for infecting bacteria. A three-dimensional cryo-EM reconstruction of the mature T4 tail ...Bacteriophage T4 and related viruses have a contractile tail that serves as an efficient mechanical device for infecting bacteria. A three-dimensional cryo-EM reconstruction of the mature T4 tail assembly at 15-A resolution shows the hexagonal dome-shaped baseplate, the extended contractile sheath, the long tail fibers attached to the baseplate and the collar formed by six whiskers that interact with the long tail fibers. Comparison with the structure of the contracted tail shows that tail contraction is associated with a substantial rearrangement of the domains within the sheath protein and results in shortening of the sheath to about one-third of its original length. During contraction, the tail tube extends beneath the baseplate by about one-half of its total length and rotates by 345 degrees , allowing it to cross the host's periplasmic space. | ||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 2bsg.cif.gz | 45.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bsg.ent.gz | 29.6 KB | Display | PDB format |
PDBx/mmJSON format | 2bsg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/2bsg ftp://data.pdbj.org/pub/pdb/validation_reports/bs/2bsg | HTTPS FTP |
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-Related structure data
Related structure data | 1126MC 1zkuC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 51909.164 Da / Num. of mol.: 3 / Source method: isolated from a natural source Details: THE PROTEIN WAS MODELED WITH SEGMENTS OF TRIPLE HELICAL COILED COIL ARRANGED ALONG CRYO-EM DENSITY ASSIGNED TO FIBRITIN Source: (natural) BACTERIOPHAGE T4 (virus) / References: UniProt: P10104 Sequence details | THE MODELED STRUCTURE DOES NOT INCLUDE LOOP REGIONS | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: T4 EXTENDED TAIL / Type: VIRUS |
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Buffer solution | pH: 7 / Details: H2O |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: COPPER GRID / Grid material: COPPER |
Vitrification | Cryogen name: ETHANE / Details: LIQUID ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM300FEG/T / Date: Jan 10, 2003 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 45000 X / Calibrated magnification: 47000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 800 nm / Cs: 2 mm |
Specimen holder | Temperature: 100 K |
Image recording | Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 75 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: EACH IMAGE | ||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||
3D reconstruction | Method: REAL SPACE SIRT / Resolution: 15 Å / Num. of particles: 3029 / Nominal pixel size: 3.97 Å / Actual pixel size: 3.97 Å / Magnification calibration: 47000 / Details: EM MAP DEPOSITED AS EMD-1126 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Details: REFINEMENT PROTOCOL--MANUAL FITTING | ||||||||||||
Atomic model building | PDB-ID: 1AA0 | ||||||||||||
Refinement | Highest resolution: 15 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 15 Å
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