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Open data
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Basic information
Entry | Database: PDB / ID: 4bij | ||||||
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Title | Threading model of T7 large terminase | ||||||
![]() | DNA MATURASE B | ||||||
![]() | HYDROLASE / ATPASE / DNA TRANSLOCATION / SINGLE-PARTICLE RECONSTRUCTION | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 16 Å | ||||||
![]() | Dauden, M.I. / Martin-Benito, J. / Sanchez-Ferrero, J.C. / Pulido-Cid, M. / Valpuesta, J.M. / Carrascosa, J.L. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 405.6 KB | Display | ![]() |
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PDB format | ![]() | 322.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2355MC ![]() 2356C ![]() 4bilC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | 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.) ![]() ![]() ![]() ![]() |
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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: FULL-LENGTH LARGE TERMINASE OF BACTERIOPHAGE T7 / Type: VIRUS / Details: STAINED WITH 2% W/V URANYL ACETATE |
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Buffer solution | Name: 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. |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO |
EM staining | Type: NEGATIVE / Material: Uranyl Acetate |
Specimen support | Details: CARBON |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Oct 23, 2009 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 67000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 1500 nm / Cs: 2.26 mm |
Image recording | Film or detector model: FEI EAGLE (4k x 4k) |
Image scans | Num. digital images: 1005 |
Radiation wavelength | Relative weight: 1 |
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Processing
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CTF correction | Details: EACH PLATE | ||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | ||||||||||||||||||
3D reconstruction | Method: 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 building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: VOLUMETRIC CORRELATION Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--HOMOLOGY MODEL BASED ON PDB 3CPE | ||||||||||||||||||
Atomic model building | PDB-ID: 3CPE Accession code: 3CPE / Source name: PDB / Type: experimental model | ||||||||||||||||||
Refinement | Highest resolution: 16 Å | ||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 16 Å
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