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Open data
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Basic information
Entry | Database: PDB / ID: 7apd | |||||||||
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Title | Bovine Papillomavirus E1 DNA helicase-replication fork complex | |||||||||
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![]() | DNA BINDING PROTEIN / DNA / virus / helicase / replisome / DNA replication. | |||||||||
Function / homology | ![]() hydrolase activity, acting on acid anhydrides / DNA helicase activity / DNA replication / DNA helicase / host cell nucleus / ATP hydrolysis activity / DNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Javed, A. / Major, B. / Stead, J. / Sanders, C.M. / Orlova, E.V. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Unwinding of a DNA replication fork by a hexameric viral helicase. Authors: Abid Javed / Balazs Major / Jonathan A Stead / Cyril M Sanders / Elena V Orlova / ![]() Abstract: Hexameric helicases are motor proteins that unwind double-stranded DNA (dsDNA) during DNA replication but how they are optimised for strand separation is unclear. Here we present the cryo-EM ...Hexameric helicases are motor proteins that unwind double-stranded DNA (dsDNA) during DNA replication but how they are optimised for strand separation is unclear. Here we present the cryo-EM structure of the full-length E1 helicase from papillomavirus, revealing all arms of a bound DNA replication fork and their interactions with the helicase. The replication fork junction is located at the entrance to the helicase collar ring, that sits above the AAA + motor assembly. dsDNA is escorted to and the 5´ single-stranded DNA (ssDNA) away from the unwinding point by the E1 dsDNA origin binding domains. The 3´ ssDNA interacts with six spirally-arranged β-hairpins and their cyclical top-to-bottom movement pulls the ssDNA through the helicase. Pulling of the RF against the collar ring separates the base-pairs, while modelling of the conformational cycle suggest an accompanying movement of the collar ring has an auxiliary role, helping to make efficient use of ATP in duplex unwinding. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 374.5 KB | Display | ![]() |
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PDB format | ![]() | 303.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 759.1 KB | Display | ![]() |
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Full document | ![]() | 811 KB | Display | |
Data in XML | ![]() | 68 KB | Display | |
Data in CIF | ![]() | 102.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11852MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 17162.084 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: OBD domains from subunits B and E. / Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 33859.172 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: DNA chain | | Mass: 12142.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5'-3' ssDNA strand of the DNA replication fork. / Source: (synth.) ![]() #4: DNA chain | | Mass: 11080.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 3'-5' ssDNA strand of the DNA replication fork. / Source: (synth.) ![]() |
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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
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Molecular weight | Value: 0.4134 MDa / Experimental value: YES | ||||||||||||||||||||||||||||
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Buffer solution | pH: 7.2 | ||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: PELCO Ultrathin Carbon with Lacey Carbon | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K Details: 3 ul of sample was applied Lacey ultra-thin carbon film grids. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Calibrated magnification: 47170 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 98 K / Temperature (min): 95 K |
Image recording | Average exposure time: 3 sec. / Electron dose: 50.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 12136 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Sampling size: 5.2 µm / Width: 5760 / Height: 4092 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 568120 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81831 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 102 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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