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- PDB-3ezk: Bacteriophage T4 gp17 motor assembly based on crystal structures ... -

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Basic information

Entry
Database: PDB / ID: 3ezk
TitleBacteriophage T4 gp17 motor assembly based on crystal structures and cryo-EM reconstructions
ComponentsDNA packaging protein Gp17
KeywordsHYDROLASE / pentameric motor / DNA packaging / Alternative initiation / ATP-binding / DNA-binding / Nuclease / Nucleotide-binding
Function / homology
Function and homology information


viral terminase, large subunit / DNA nuclease activity / viral genome packaging / viral procapsid maturation / viral DNA genome packaging / nuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / chromosome organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity ...viral terminase, large subunit / DNA nuclease activity / viral genome packaging / viral procapsid maturation / viral DNA genome packaging / nuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / chromosome organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Terminase, large subunit, gp17-like / Terminase, large subunit gp17-like, C-terminal / Terminase RNaseH-like domain / Terminase large subunit, T4likevirus-type, N-terminal / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Terminase, large subunit
Similarity search - Component
Biological speciesBacteriophage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 34 Å
AuthorsSun, S. / Rossmann, M.G.
CitationJournal: Cell / Year: 2008
Title: The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces.
Authors: Siyang Sun / Kiran Kondabagil / Bonnie Draper / Tanfis I Alam / Valorie D Bowman / Zhihong Zhang / Shylaja Hegde / Andrei Fokine / Michael G Rossmann / Venigalla B Rao /
Abstract: Viral genomes are packaged into "procapsids" by powerful molecular motors. We report the crystal structure of the DNA packaging motor protein, gene product 17 (gp17), in bacteriophage T4. The ...Viral genomes are packaged into "procapsids" by powerful molecular motors. We report the crystal structure of the DNA packaging motor protein, gene product 17 (gp17), in bacteriophage T4. The structure consists of an N-terminal ATPase domain, which provides energy for compacting DNA, and a C-terminal nuclease domain, which terminates packaging. We show that another function of the C-terminal domain is to translocate the genome into the procapsid. The two domains are in close contact in the crystal structure, representing a "tensed state." A cryo-electron microscopy reconstruction of the T4 procapsid complexed with gp17 shows that the packaging motor is a pentamer and that the domains within each monomer are spatially separated, representing a "relaxed state." These structures suggest a mechanism, supported by mutational and other data, in which electrostatic forces drive the DNA packaging by alternating between tensed and relaxed states. Similar mechanisms may occur in other molecular motors.
History
DepositionOct 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Dec 27, 2023Group: 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_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

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Assembly

Deposited unit
A: DNA packaging protein Gp17
B: DNA packaging protein Gp17
C: DNA packaging protein Gp17
D: DNA packaging protein Gp17
E: DNA packaging protein Gp17


Theoretical massNumber of molelcules
Total (without water)331,0205
Polymers331,0205
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
DNA packaging protein Gp17 / Terminase / Coordinate model: Cα atoms only


Mass: 66204.062 Da / Num. of mol.: 5 / Fragment: Residues 1-577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage T4 (virus) / Strain: D / Gene: 17 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17312

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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: T4 procapsid with gp17 bound / Type: VIRUS
Buffer solutionName: 50mM Tris-HCl, 100mM NaCl, 5mM MgCl2, 3mM beta-Mercaptoethanol
pH: 7.4
Details: 50mM Tris-HCl, 100mM NaCl, 5mM MgCl2, 3mM beta-Mercaptoethanol
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: flash-frozen on holey grids in liquid ethane

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 38000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1EMfitmodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: phase flipping of each micrograph
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionMethod: Spider / Resolution: 34 Å / Num. of particles: 1716 / Nominal pixel size: 6.48 Å / Actual pixel size: 6.48 Å / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Sumf
Details: METHOD--N- and C-terminal domains were separately fitted into their corresponding cryoEM densities REFINEMENT PROTOCOL--Rigid body
Atomic model buildingPDB-ID: 3CPE

3cpe


Accession code: 3CPE / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms2765 0 0 0 2765

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