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Yorodumi- EMDB-15341: Human replisome bound by pol alpha, engaged on fork DNA containin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15341 | |||||||||
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Title | Human replisome bound by pol alpha, engaged on fork DNA containing a 60 nt lagging strand. | |||||||||
Map data | Human replisome bound by pol alpha, engaged on fork DNA containing a 60 nt lagging strand. | |||||||||
Sample |
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Keywords | Replication / helicase / polymerase / pol alpha / priming | |||||||||
Function / homology | Function and homology information positive regulation of DNA primase activity / cellular response to bleomycin / DNA primase AEP / ribonucleotide binding / DNA secondary structure binding / Switching of origins to a post-replicative state / detection of abiotic stimulus / replication fork arrest / regulation of nuclear cell cycle DNA replication / Unwinding of DNA ...positive regulation of DNA primase activity / cellular response to bleomycin / DNA primase AEP / ribonucleotide binding / DNA secondary structure binding / Switching of origins to a post-replicative state / detection of abiotic stimulus / replication fork arrest / regulation of nuclear cell cycle DNA replication / Unwinding of DNA / DNA replication initiation / cell cycle phase transition / cellular response to cisplatin / DNA/RNA hybrid binding / GINS complex / DNA strand elongation involved in mitotic DNA replication / mitotic DNA replication preinitiation complex assembly / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / nuclear origin of replication recognition complex / cellular response to hydroxyurea / alpha DNA polymerase:primase complex / Polymerase switching / mitotic DNA replication / regulation of type I interferon production / Processive synthesis on the lagging strand / anaphase-promoting complex binding / CMG complex / DNA replication checkpoint signaling / single-stranded 3'-5' DNA helicase activity / entrainment of circadian clock / DNA primase activity / Removal of the Flap Intermediate / regulation of phosphorylation / MCM complex / DNA replication preinitiation complex / Polymerase switching on the C-strand of the telomere / lagging strand elongation / DNA replication, synthesis of primer / replication fork protection complex / mitotic DNA replication checkpoint signaling / mitotic DNA replication initiation / double-strand break repair via break-induced replication / mitotic intra-S DNA damage checkpoint signaling / positive regulation of double-strand break repair / regulation of DNA-templated DNA replication initiation / single-stranded DNA helicase activity / inner cell mass cell proliferation / DNA strand elongation involved in DNA replication / branching morphogenesis of an epithelial tube / DNA synthesis involved in DNA repair / cochlea development / G1/S-Specific Transcription / activation of protein kinase activity / leading strand elongation / replication fork processing / Apoptotic cleavage of cellular proteins / DNA unwinding involved in DNA replication / nuclear replication fork / mitotic G2 DNA damage checkpoint signaling / 3'-5' DNA helicase activity / DNA replication origin binding / positive regulation of double-strand break repair via homologous recombination / Activation of the pre-replicative complex / DNA replication initiation / cellular response to interleukin-4 / Activation of ATR in response to replication stress / response to UV / ciliary basal body / DNA damage checkpoint signaling / Defective pyroptosis / Assembly of the pre-replicative complex / morphogenesis of an epithelium / lung development / regulation of circadian rhythm / DNA-templated DNA replication / nuclear matrix / double-strand break repair via nonhomologous end joining / Orc1 removal from chromatin / circadian rhythm / protein import into nucleus / nucleosome assembly / cellular response to xenobiotic stimulus / nuclear envelope / site of double-strand break / mitotic cell cycle / single-stranded DNA binding / Processing of DNA double-strand break ends / 4 iron, 4 sulfur cluster binding / histone binding / peptidyl-serine phosphorylation / DNA replication / DNA helicase / cell population proliferation / chromosome, telomeric region / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / Ub-specific processing proteases / cell cycle / cell division Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Jones ML / Yeeles JTP | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Mol Cell / Year: 2023 Title: How Pol α-primase is targeted to replisomes to prime eukaryotic DNA replication. Authors: Morgan L Jones / Valentina Aria / Yasemin Baris / Joseph T P Yeeles / Abstract: During eukaryotic DNA replication, Pol α-primase generates primers at replication origins to start leading-strand synthesis and every few hundred nucleotides during discontinuous lagging-strand ...During eukaryotic DNA replication, Pol α-primase generates primers at replication origins to start leading-strand synthesis and every few hundred nucleotides during discontinuous lagging-strand replication. How Pol α-primase is targeted to replication forks to prime DNA synthesis is not fully understood. Here, by determining cryoelectron microscopy (cryo-EM) structures of budding yeast and human replisomes containing Pol α-primase, we reveal a conserved mechanism for the coordination of priming by the replisome. Pol α-primase binds directly to the leading edge of the CMG (CDC45-MCM-GINS) replicative helicase via a complex interaction network. The non-catalytic PRIM2/Pri2 subunit forms two interfaces with CMG that are critical for in vitro DNA replication and yeast cell growth. These interactions position the primase catalytic subunit PRIM1/Pri1 directly above the exit channel for lagging-strand template single-stranded DNA (ssDNA), revealing why priming occurs efficiently only on the lagging-strand template and elucidating a mechanism for Pol α-primase to overcome competition from RPA to initiate primer synthesis. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15341.map.gz | 6.7 MB | EMDB map data format | |
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Header (meta data) | emd-15341-v30.xml emd-15341.xml | 11.8 KB 11.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15341_fsc.xml | 11.9 KB | Display | FSC data file |
Images | emd_15341.png | 105.7 KB | ||
Others | emd_15341_half_map_1.map.gz emd_15341_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15341 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15341 | HTTPS FTP |
-Validation report
Summary document | emd_15341_validation.pdf.gz | 802.3 KB | Display | EMDB validaton report |
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Full document | emd_15341_full_validation.pdf.gz | 801.8 KB | Display | |
Data in XML | emd_15341_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | emd_15341_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15341 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15341 | HTTPS FTP |
-Related structure data
Related structure data | 8b9dMC 8b9aC 8b9bC 8b9cC 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_15341.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Human replisome bound by pol alpha, engaged on fork DNA containing a 60 nt lagging strand. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.2363 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A
File | emd_15341_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_15341_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Replisome - pol alpha complex
Entire | Name: Replisome - pol alpha complex |
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Components |
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-Supramolecule #1: Replisome - pol alpha complex
Supramolecule | Name: Replisome - pol alpha complex / type: complex / ID: 1 / Parent: 0 Details: S. cerevisiae pol alpha bound to the core replisome engaged with a fork DNA substrate containing a 60 nucleotide lagging strand. |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.184 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |