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- PDB-8v6i: DNA elongation complex (configuration 1) of Xenopus laevis DNA po... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8v6i | ||||||||||||
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Title | DNA elongation complex (configuration 1) of Xenopus laevis DNA polymerase alpha-primase | ||||||||||||
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Function / homology | ![]() alpha DNA polymerase:primase complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Mullins, E.A. / Durie, C.L. / Ohi, M.D. / Chazin, W.J. / Eichman, B.F. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A mechanistic model of primer synthesis from catalytic structures of DNA polymerase α-primase. Authors: Elwood A Mullins / Lauren E Salay / Clarissa L Durie / Noah P Bradley / Jane E Jackman / Melanie D Ohi / Walter J Chazin / Brandt F Eichman / ![]() Abstract: The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is ...The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is unknown. Here, we report cryo-EM structures of Xenopus laevis polα-primase in complex with primed templates representing various stages of DNA synthesis. Our data show how interaction of the primase regulatory subunit with the primer 5' end facilitates handoff of the primer to polα and increases polα processivity, thereby regulating both RNA and DNA composition. The structures detail how flexibility within the heterotetramer enables synthesis across two active sites and provide evidence that termination of DNA synthesis is facilitated by reduction of polα and primase affinities for the varied conformations along the chimeric primer-template duplex. Together, these findings elucidate a critical catalytic step in replication initiation and provide a comprehensive model for primer synthesis by polα-primase. #1: ![]() Title: A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase Authors: Mullins, E.A. / Salay, L.E. / Durie, C.L. / Bradley, N.P. / Jackman, J.E. / Ohi, M.D. / Chazin, W.J. / Eichman, B.F. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 886.6 KB | Display | ![]() |
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PDB format | ![]() | 717.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 42992MC ![]() 8g99C ![]() 8g9fC ![]() 8g9lC ![]() 8g9nC ![]() 8g9oC ![]() 8ucuC ![]() 8ucvC ![]() 8ucwC ![]() 8v5mC ![]() 8v5nC ![]() 8v5oC ![]() 8v6gC ![]() 8v6hC ![]() 8v6jC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-DNA polymerase alpha ... , 2 types, 2 molecules AB
#1: Protein | Mass: 129009.414 Da / Num. of mol.: 1 / Fragment: UNP residues 335-1458 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 67194.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-Protein , 2 types, 2 molecules CD
#3: Protein | ![]() Mass: 59673.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#4: Protein | ![]() Mass: 49356.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-DNA chain / DNA/RNA hybrid , 2 types, 2 molecules EF
#5: DNA chain | Mass: 15458.913 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: DNA/RNA hybrid | Mass: 6433.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 7 molecules ![](data/chem/img/ZN.gif)
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#7: Chemical | #8: Chemical | ChemComp-DGT / | ![]() #9: Chemical | #10: Chemical | ChemComp-SF4 / | ![]() |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | |||||||||||||||||||||||||||||||||||
Specimen | Conc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | |||||||||||||||||||||||||||||||||||
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 13641 |
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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: 8928051 | |||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | |||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 14.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4441 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | |||||||||||||||||||||||||||
Atomic model building |
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