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Yorodumi- PDB-1tja: Fitting of gp8, gp9, and gp11 into the cryo-EM reconstruction of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tja | ||||||
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Title | Fitting of gp8, gp9, and gp11 into the cryo-EM reconstruction of the bacteriophage T4 contracted tail | ||||||
Components |
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Keywords | VIRAL PROTEIN / fitting / docking / cryo-EM / gp8 / gp9 / gp11 / circular symmetry | ||||||
Function / homology | Function and homology information virus tail, baseplate / viral tail assembly / viral release from host cell Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 16 Å | ||||||
Authors | Leiman, P.G. / Chipman, P.R. / Kostyuchenko, V.A. / Mesyanzhinov, V.V. / Rossmann, M.G. | ||||||
Citation | Journal: Cell / Year: 2004 Title: Three-dimensional rearrangement of proteins in the tail of bacteriophage T4 on infection of its host. Authors: Petr G Leiman / Paul R Chipman / Victor A Kostyuchenko / Vadim V Mesyanzhinov / Michael G Rossmann / Abstract: The contractile tail of bacteriophage T4 undergoes major structural transitions when the virus attaches to the host cell surface. The baseplate at the distal end of the tail changes from a hexagonal ...The contractile tail of bacteriophage T4 undergoes major structural transitions when the virus attaches to the host cell surface. The baseplate at the distal end of the tail changes from a hexagonal to a star shape. This causes the sheath around the tail tube to contract and the tail tube to protrude from the baseplate and pierce the outer cell membrane and the cell wall before reaching the inner cell membrane for subsequent viral DNA injection. Analogously, the T4 tail can be contracted by treatment with 3 M urea. The structure of the T4 contracted tail, including the head-tail joining region, has been determined by cryo-electron microscopy to 17 A resolution. This 1200 A-long, 20 MDa structure has been interpreted in terms of multiple copies of its approximately 20 component proteins. A comparison with the metastable hexagonal baseplate of the mature virus shows that the baseplate proteins move as rigid bodies relative to each other during the structural change. | ||||||
History |
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Remark 999 | SEQUENCE COORDINATES FOR CA ATOMS ONLY WERE SUBMITTED. |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 1tja.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tja.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 1tja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tja_validation.pdf.gz | 837.4 KB | Display | wwPDB validaton report |
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Full document | 1tja_full_validation.pdf.gz | 836.9 KB | Display | |
Data in XML | 1tja_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 1tja_validation.cif.gz | 44.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/1tja ftp://data.pdbj.org/pub/pdb/validation_reports/tj/1tja | HTTPS FTP |
-Related structure data
Related structure data | 1086MC 1089MC 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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Symmetry | Point symmetry: (Hermann–Mauguin notation: 6 / Schoenflies symbol: C6 (6 fold cyclic)) |
-Components
#1: Protein | Mass: 38041.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Strain: D / References: UniProt: P19062 #2: Protein | Mass: 31024.725 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Strain: D / References: UniProt: P10927 #3: Protein | Mass: 23725.523 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Strain: D / References: UniProt: P10929 |
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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 |
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Details of virus | Host category: BACTERIA(EUBACTERIA) / Isolate: STRAIN / Type: VIRION | |||||||||||||||||||||||||
Natural host | Organism: Escherichia coli | |||||||||||||||||||||||||
Buffer solution | Name: H2O / pH: 7.5 / Details: H2O | |||||||||||||||||||||||||
Specimen | Conc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM300FEG/T / Date: Jan 6, 2002 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 45000 X / Calibrated magnification: 47000 X / Nominal defocus max: 3400 nm / Nominal defocus min: 500 nm / Cs: 1.4 mm |
Specimen holder | Temperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
EM software |
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CTF correction | Details: CTF correction of each particle | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Method: Back projection / Resolution: 16 Å / Num. of particles: 1965 / Nominal pixel size: 4.10442 Å / Actual pixel size: 3.93285 Å / Magnification calibration: Catalase crystals diffraction / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Details: METHOD--Laplacian filtered real space | ||||||||||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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