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Yorodumi- EMDB-42993: DNA elongation complex (configuration 2) of Xenopus laevis DNA po... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42993 | ||||||||||||
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Title | DNA elongation complex (configuration 2) of Xenopus laevis DNA polymerase alpha-primase | ||||||||||||
Map data | DNA elongation complex (configuration 2) of Xenopus laevis DNA polymerase alpha-primase | ||||||||||||
Sample |
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Keywords | Primase / DNA polymerase / chimeric RNA-DNA primer / RNA/DNA hybrid / DNA replication / DNA synthesis / REPLICATION / TRANSFERASE-DNA-RNA complex | ||||||||||||
Function / homology | Function and homology information alpha DNA polymerase:primase complex / DNA primase activity / primosome complex / DNA replication, synthesis of primer / lagging strand elongation / mitotic DNA replication initiation / DNA strand elongation involved in DNA replication / leading strand elongation / DNA replication initiation / DNA-directed RNA polymerase complex ...alpha DNA polymerase:primase complex / DNA primase activity / primosome complex / DNA replication, synthesis of primer / lagging strand elongation / mitotic DNA replication initiation / DNA strand elongation involved in DNA replication / leading strand elongation / DNA replication initiation / DNA-directed RNA polymerase complex / double-strand break repair via nonhomologous end joining / nuclear matrix / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nuclear envelope / 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 | Xenopus laevis (African clawed frog) / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.11 Å | ||||||||||||
Authors | Mullins EA / Durie CL / Ohi MD / Chazin WJ / Eichman BF | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 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: Journal: To Be Published Title: A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase Authors: Mullins EA / Salay LE / Durie CL / Bradley NP / Jackman JE / Ohi MD / Chazin WJ / Eichman BF | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42993.map.gz | 917 KB | EMDB map data format | |
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Header (meta data) | emd-42993-v30.xml emd-42993.xml | 28.4 KB 28.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42993_fsc.xml | 2.4 KB | Display | FSC data file |
Images | emd_42993.png | 25.7 KB | ||
Filedesc metadata | emd-42993.cif.gz | 8.6 KB | ||
Others | emd_42993_half_map_1.map.gz emd_42993_half_map_2.map.gz | 952.5 KB 952.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42993 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42993 | HTTPS FTP |
-Validation report
Summary document | emd_42993_validation.pdf.gz | 547.7 KB | Display | EMDB validaton report |
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Full document | emd_42993_full_validation.pdf.gz | 547.2 KB | Display | |
Data in XML | emd_42993_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | emd_42993_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42993 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42993 | HTTPS FTP |
-Related structure data
Related structure data | 8v6jMC 8g99C 8g9fC 8g9lC 8g9nC 8g9oC 8ucuC 8ucvC 8ucwC 8v5mC 8v5nC 8v5oC 8v6gC 8v6hC 8v6iC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_42993.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | DNA elongation complex (configuration 2) of Xenopus laevis DNA polymerase alpha-primase | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.11875 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: DNA elongation complex (configuration 2) of Xenopus laevis...
File | emd_42993_half_map_1.map | ||||||||||||
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Annotation | DNA elongation complex (configuration 2) of Xenopus laevis DNA polymerase alpha-primase (half 1) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: DNA elongation complex (configuration 2) of Xenopus laevis...
File | emd_42993_half_map_2.map | ||||||||||||
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Annotation | DNA elongation complex (configuration 2) of Xenopus laevis DNA polymerase alpha-primase (half 2) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Polymerase alpha-primase with a DNA elongation substrate
+Supramolecule #1: Polymerase alpha-primase with a DNA elongation substrate
+Supramolecule #2: Polymerase alpha
+Supramolecule #3: Primase
+Supramolecule #4: DNA elongation substrate
+Macromolecule #1: DNA polymerase alpha catalytic subunit
+Macromolecule #2: DNA polymerase alpha subunit B
+Macromolecule #3: DNA primase large subunit
+Macromolecule #4: DNA primase
+Macromolecule #5: DNA template
+Macromolecule #6: RNA-DNA primer
+Macromolecule #7: ZINC ION
+Macromolecule #8: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.9 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-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: 3 / Number real images: 13641 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
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 |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT | ||||||
Output model | PDB-8v6j: |