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- PDB-3j0h: Fitting of the bacteriophage phiKZ gp29PR structure into the cryo... -

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Basic information

Entry
Database: PDB / ID: 3j0h
TitleFitting of the bacteriophage phiKZ gp29PR structure into the cryo-EM density map of the phiKZ extended tail sheath
ComponentsPHIKZ029
KeywordsSTRUCTURAL PROTEIN
Function / homology: / Bacteriophage phiKZ, gp29PR / PHIKZ029
Function and homology information
Biological speciesPseudomonas phage phiKZ (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 18 Å
AuthorsAksyuk, A.A. / Fokine, A. / Kurochkina, L.P. / Mesyanzhinov, V.V. / Rossmann, M.G.
CitationJournal: Structure / Year: 2011
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.
History
DepositionAug 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Other
Revision 1.3Jul 23, 2014Group: Other
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_database_related / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_database_related.content_type

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: PHIKZ029
B: PHIKZ029
C: PHIKZ029
D: PHIKZ029
E: PHIKZ029
F: PHIKZ029


Theoretical massNumber of molelcules
Total (without water)193,7816
Polymers193,7816
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
PHIKZ029


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) Pseudomonas phage phiKZ (virus) / References: UniProt: Q8SDD3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bacteriophage phiKZ extended tail sheath / Type: VIRUS / Details: tail portion of the virion was selected
Details of virusHost category: BACTERIA(EUBACTERIA) / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Pseudomonas aeruginosa
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Details: liquid ethane

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/HE / Date: Aug 16, 2004
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EMfitmodel fitting
2SPIDER3D reconstruction
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionMethod: Spider single particle / Resolution: 18 Å / Resolution method: FSC 0.5 CUT-OFF / Nominal pixel size: 4.24 Å / Actual pixel size: 4.24 Å / Details: FSC at 0.5 cut-off / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 3SPE

3spe


Accession code: 3SPE / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms11646 0 0 0 11646

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