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- EMDB-29871: DNA initiation subcomplex of Xenopus laevis DNA polymerase alpha-... -
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Open data
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Basic information
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Title | DNA initiation subcomplex of Xenopus laevis DNA polymerase alpha-primase | ||||||||||||
![]() | DNA initiation subcomplex of Xenopus laevis DNA polymerase alpha-primase | ||||||||||||
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![]() | Primase / DNA polymerase / chimeric RNA-DNA primer / RNA/DNA hybrid / DNA replication / DNA synthesis / REPLICATION / TRANSFERASE-DNA-RNA complex | ||||||||||||
Function / homology | ![]() alpha DNA polymerase:primase complex / lagging strand elongation / DNA replication, synthesis of primer / mitotic DNA replication initiation / DNA strand elongation involved in DNA replication / leading strand elongation / DNA replication origin binding / DNA replication initiation / nuclear matrix / double-strand break repair via nonhomologous end joining ...alpha DNA polymerase:primase complex / lagging strand elongation / DNA replication, synthesis of primer / mitotic DNA replication initiation / DNA strand elongation involved in DNA replication / leading strand elongation / DNA replication origin binding / DNA replication initiation / nuclear matrix / double-strand break repair via nonhomologous end joining / nuclear envelope / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / chromatin binding / chromatin / nucleolus / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
![]() | Mullins EA / Durie CL / Ohi MD / Chazin WJ / Eichman BF | ||||||||||||
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 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. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 140.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 28.6 KB 28.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 21.2 KB | ||
Filedesc metadata | ![]() | 8 KB | ||
Others | ![]() ![]() ![]() | 157.9 MB 140.6 MB 140.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 766 KB | Display | ![]() |
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Full document | ![]() | 765.5 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 26.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8g9lMC ![]() 8g99C ![]() 8g9fC ![]() 8g9nC ![]() 8g9oC ![]() 8ucuC ![]() 8ucvC ![]() 8ucwC ![]() 8v5mC ![]() 8v5nC ![]() 8v5oC ![]() 8v6gC ![]() 8v6hC ![]() 8v6iC ![]() 8v6jC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | DNA initiation subcomplex of Xenopus laevis DNA polymerase alpha-primase | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.91 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: DNA initiation subcomplex of Xenopus laevis DNA polymerase...
File | emd_29871_additional_1.map | ||||||||||||
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Annotation | DNA initiation subcomplex of Xenopus laevis DNA polymerase alpha-primase (locally sharpened) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: DNA initiation subcomplex of Xenopus laevis DNA polymerase...
File | emd_29871_half_map_1.map | ||||||||||||
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Annotation | DNA initiation subcomplex of Xenopus laevis DNA polymerase alpha-primase (half 2) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: DNA initiation subcomplex of Xenopus laevis DNA polymerase...
File | emd_29871_half_map_2.map | ||||||||||||
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Annotation | DNA initiation subcomplex of Xenopus laevis DNA polymerase alpha-primase (half 1) | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Polymerase alpha-primase with a DNA initiation substrate
+Supramolecule #1: Polymerase alpha-primase with a DNA initiation substrate
+Supramolecule #2: Polymerase alpha
+Supramolecule #3: Primase
+Supramolecule #4: DNA initiation substrate
+Macromolecule #1: DNA polymerase alpha catalytic subunit
+Macromolecule #2: DNA primase large subunit
+Macromolecule #3: DNA template
+Macromolecule #4: RNA primer
+Macromolecule #5: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #6: MAGNESIUM ION
+Macromolecule #7: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.9 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 4 / Number real images: 12845 / Average electron dose: 50.7 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 45000 |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |