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- PDB-3j0i: Fitting of the phiKZ gp29PR structure into the cryo-EM density ma... -
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Basic information
Entry | Database: PDB / ID: 3j0i | ||||||
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Title | Fitting of the phiKZ gp29PR structure into the cryo-EM density map of the phiKZ polysheath | ||||||
![]() | PHIKZ029 | ||||||
![]() | STRUCTURAL PROTEIN / bacteriophage tail sheath | ||||||
Function / homology | : / Bacteriophage phiKZ, gp29PR / PHIKZ029![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 19 Å | ||||||
![]() | Aksyuk, A.A. / Fokine, A. / Kurochkina, L.P. / Mesyanzhinov, V.V. / Rossmann, M.G. | ||||||
![]() | ![]() Title: Structural conservation of the myoviridae phage tail sheath protein fold. Authors: Anastasia A Aksyuk / Lidia P Kurochkina / Andrei Fokine / Farhad Forouhar / Vadim V Mesyanzhinov / Liang Tong / Michael G Rossmann / ![]() Abstract: Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 Å diameter icosahedral head and a 2000 Å-long contractile tail. The ...Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 Å diameter icosahedral head and a 2000 Å-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a tail sheath protein fragment of phiKZ was determined to 2.4 Å resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 Å resolution. Despite low sequence identity between these proteins, all of these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 577.7 KB | Display | ![]() |
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PDB format | ![]() | 480.9 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 787.6 KB | Display | ![]() |
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Full document | ![]() | 825.4 KB | Display | |
Data in XML | ![]() | 48.1 KB | Display | |
Data in CIF | ![]() | 63.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5331MC ![]() 5332C ![]() 3j0hC ![]() 3speC C: citing same article ( M: map data used to model this data |
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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: 32296.910 Da / Num. of mol.: 6 Fragment: protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390) 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: Bacteriophage phiKZ polysheath / Type: VIRUS / Details: tail portion of the virion was selected |
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Details of virus | Host category: BACTERIA(EUBACTERIA) / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Pseudomonas aeruginosa |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Details: liquid ethane |
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Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM200FEG |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||
3D reconstruction | Method: spider single particle / Resolution: 19 Å / Resolution method: FSC 0.5 CUT-OFF / Nominal pixel size: 2.49 Å / Actual pixel size: 2.49 Å / Details: FSC at 0.5 cut-off / Symmetry type: POINT | ||||||||||||
Atomic model building | Space: REAL | ||||||||||||
Atomic model building | PDB-ID: 3SPE Accession code: 3SPE / Source name: PDB / Type: experimental model | ||||||||||||
Refinement step | Cycle: LAST
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