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- PDB-4bij: Threading model of T7 large terminase -

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Basic information

Entry
Database: PDB / ID: 4bij
TitleThreading model of T7 large terminase
ComponentsDNA MATURASE B
KeywordsHYDROLASE / ATPASE / DNA TRANSLOCATION / SINGLE-PARTICLE RECONSTRUCTION
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 / 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: 16 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
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

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-2355
  • Imaged by UCSF Chimera
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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
Water0
1


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

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Components

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


Mass: 53822.504 Da / Num. of mol.: 5
Fragment: FRAGMENT WITH 110 AMINOACIDS DELETION, 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: FULL-LENGTH LARGE TERMINASE OF BACTERIOPHAGE T7 / Type: VIRUS / Details: STAINED WITH 2% W/V URANYL ACETATE
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: Oct 23, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / 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: 1005
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 / Resolution: 16 Å / Num. of particles: 3650 / Actual pixel size: 4.4 Å
Details: 3CPE PBD WAS USED AS A TEMPLATE FOR THE GENERATION OF THE GP19 ATOMIC MODEL THAT WAS SYMMETRIZED TO 5 AND FITTED IN THE LARGE TERMINASE EM VOLUME. SUBMISSION BASED ON EXPERIMENTAL DATA FROM ...Details: 3CPE PBD WAS USED AS A TEMPLATE FOR THE GENERATION OF THE GP19 ATOMIC MODEL THAT WAS SYMMETRIZED TO 5 AND FITTED IN THE LARGE TERMINASE EM VOLUME. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2355. (DEPOSITION ID: 11611).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: VOLUMETRIC CORRELATION
Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--HOMOLOGY MODEL BASED ON PDB 3CPE
Atomic model buildingPDB-ID: 3CPE
RefinementHighest resolution: 16 Å
Refinement stepCycle: LAST / Highest resolution: 16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18855 0 0 0 18855

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