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- PDB-4bil: Threading model of the T7 large terminase within the gp8gp19 complex -

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Basic information

Entry
Database: PDB / ID: 4bil
TitleThreading model of the T7 large terminase within the gp8gp19 complex
ComponentsDNA MATURASE B
KeywordsHYDROLASE / PACKAGING MOTOR / CONNECTOR / DNA TRANSLOCATION / ATPASE.
Function / homology
Function and homology information


viral terminase, large subunit / viral DNA genome packaging / 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 gp19 / : / Terminase Bacteriophage T7, Ribonuclease H-like domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Terminase, large subunit
Similarity search - Component
Biological speciesENTEROBACTERIA PHAGE T7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 29 Å
AuthorsDauden, M.I. / Martin-Benito, J. / Sanchez-Ferrero, J.C. / Pulido-Cid, M. / Valpuesta, J.M. / Carrascosa, J.L.
CitationJournal: J Biol Chem / Year: 2013
Title: Large terminase conformational change induced by connector binding in bacteriophage T7.
Authors: María I Daudén / Jaime Martín-Benito / Juan C Sánchez-Ferrero / Mar Pulido-Cid / José M Valpuesta / José L Carrascosa /
Abstract: During bacteriophage morphogenesis DNA is translocated into a preformed prohead by the complex formed by the portal protein, or connector, plus the terminase, which are located at an especial prohead ...During bacteriophage morphogenesis DNA is translocated into a preformed prohead by the complex formed by the portal protein, or connector, plus the terminase, which are located at an especial prohead vertex. The terminase is a powerful motor that converts ATP hydrolysis into mechanical movement of the DNA. Here, we have determined the structure of the T7 large terminase by electron microscopy. The five terminase subunits assemble in a toroid that encloses a channel wide enough to accommodate dsDNA. The structure of the complete connector-terminase complex is also reported, revealing the coupling between the terminase and the connector forming a continuous channel. The structure of the terminase assembled into the complex showed a different conformation when compared with the isolated terminase pentamer. To understand in molecular terms the terminase morphological change, we generated the terminase atomic model based on the crystallographic structure of its phage T4 counterpart. The docking of the threaded model in both terminase conformations showed that the transition between the two states can be achieved by rigid body subunit rotation in the pentameric assembly. The existence of two terminase conformations and its possible relation to the sequential DNA translocation may shed light into the molecular bases of the packaging mechanism of bacteriophage T7.
History
DepositionApr 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references / Other / Structure summary
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Apr 19, 2017Group: Other
Revision 1.4Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.5May 8, 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_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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  • Simplified surface model + fitted atomic model
  • EMDB-2356
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  • EMDB-2356
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Assembly

Deposited unit
A: DNA MATURASE B
B: DNA MATURASE B
C: DNA MATURASE B
D: DNA MATURASE B
E: DNA MATURASE B


Theoretical massNumber of molelcules
Total (without water)269,1135
Polymers269,1135
Non-polymers00
Water00
1


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

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Components

#1: Protein
DNA MATURASE B / DNA-PACKAGING PROTEIN B / GP19 / LARGE TERMINASE


Mass: 53822.504 Da / Num. of mol.: 5 / Fragment: RESIDUES 1-476
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIA PHAGE T7 (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS / References: UniProt: P03694

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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: GP8GP19 COMPLEX OF BACTERIOPHAGE T7 / Type: VIRUS
Buffer solutionName: 50 MM SODIUM PHOSPHATE BUFFER PH 7, 300 MM NACL, 10 MM MGCL2, 1 MM ADP 5 MM DTT AND 20% (V/V) GLYCEROL
pH: 7.4
Details: 50 MM SODIUM PHOSPHATE BUFFER PH 7, 300 MM NACL, 10 MM MGCL2, 1 MM ADP 5 MM DTT AND 20% (V/V) GLYCEROL
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: uranyl acetate
Specimen supportDetails: CARBON

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jul 7, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 67000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 1500 nm / Cs: 2.26 mm
Image recordingFilm or detector model: FEI EAGLE (4k x 4k)
Image scansNum. digital images: 573
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Situsmodel fitting
2UCSF Chimeramodel fitting
3EMAN3D reconstruction
4SPIDER3D reconstruction
5Xmipp3D reconstruction
CTF correctionDetails: EACH PLATE
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionMethod: COMMON LINES AND PROJECTION MATCHING / Resolution: 29 Å / Num. of particles: 837 / Actual pixel size: 4.2 Å
Details: 3CPE PDB WAS USED AS TEMPLATE FOR THE GENERATION OF THE THREADING MODEL OF GP19 WITHIN THE GP19GP8 COMPLEX SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2356. (DEPOSITION ID: 11615).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--THREADING MODEL
Atomic model buildingPDB-ID: 3CPE

3cpe


Accession code: 3CPE / Source name: PDB / Type: experimental model
RefinementHighest resolution: 29 Å
Refinement stepCycle: LAST / Highest resolution: 29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18925 0 0 0 18925

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