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Yorodumi- EMDB-15923: Human replisome prepared in the presence of a fork DNA substrate ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15923 | |||||||||
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Title | Human replisome prepared in the presence of a fork DNA substrate containing a 60 nucleotide lagging strand. Off DNA. | |||||||||
Map data | Human replisome prepared in the presence of a fork DNA substrate containing a 60 nucleotide lagging strand. Off DNA. Locally filtered | |||||||||
Sample |
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Keywords | human / replication / priming / polymerase | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 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_15923.map.gz | 7.8 MB | EMDB map data format | |
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Header (meta data) | emd-15923-v30.xml emd-15923.xml | 19.3 KB 19.3 KB | Display Display | EMDB header |
Images | emd_15923.png | 120.4 KB | ||
Others | emd_15923_additional_1.map.gz emd_15923_additional_2.map.gz emd_15923_half_map_1.map.gz emd_15923_half_map_2.map.gz | 118.1 MB 63 MB 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15923 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15923 | HTTPS FTP |
-Validation report
Summary document | emd_15923_validation.pdf.gz | 857.1 KB | Display | EMDB validaton report |
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Full document | emd_15923_full_validation.pdf.gz | 856.6 KB | Display | |
Data in XML | emd_15923_validation.xml.gz | 14 KB | Display | |
Data in CIF | emd_15923_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15923 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15923 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15923.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Human replisome prepared in the presence of a fork DNA substrate containing a 60 nucleotide lagging strand. Off DNA. Locally filtered | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Human replisome prepared in the presence of a...
File | emd_15923_additional_1.map | ||||||||||||
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Annotation | Human replisome prepared in the presence of a fork DNA substrate containing a 60 nucleotide lagging strand. Off DNA. Sharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Human replisome prepared in the presence of a...
File | emd_15923_additional_2.map | ||||||||||||
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Annotation | Human replisome prepared in the presence of a fork DNA substrate containing a 60 nucleotide lagging strand. Off DNA. Unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Human replisome prepared in the presence of a...
File | emd_15923_half_map_1.map | ||||||||||||
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Annotation | Human replisome prepared in the presence of a fork DNA substrate containing a 60 nucleotide lagging strand. Off DNA. Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Human replisome prepared in the presence of a...
File | emd_15923_half_map_2.map | ||||||||||||
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Annotation | Human replisome prepared in the presence of a fork DNA substrate containing a 60 nucleotide lagging strand. Off DNA. Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human replisome bound by pol alpha, engaged on a fork DNA substra...
Entire | Name: Human replisome bound by pol alpha, engaged on a fork DNA substrate with a 60 nucleotide lagging strand. |
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Components |
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-Supramolecule #1: Human replisome bound by pol alpha, engaged on a fork DNA substra...
Supramolecule | Name: Human replisome bound by pol alpha, engaged on a fork DNA substrate with a 60 nucleotide lagging strand. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#21 |
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Source (natural) | Organism: Homo sapiens (human) |
-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 BIOQUANTUM (6k x 4k) / Average electron dose: 37.8 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: 3.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74940 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |