+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37345 | |||||||||||||||||||||||||||
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Title | Yeast replisome in state IV | |||||||||||||||||||||||||||
Map data | ||||||||||||||||||||||||||||
Sample |
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Keywords | replisome / complex / DNA replication / REPLICATION | |||||||||||||||||||||||||||
Function / homology | Function and homology information establishment of sister chromatid cohesion / DNA-templated DNA replication maintenance of fidelity / Unwinding of DNA / DNA replication initiation / Cul8-RING ubiquitin ligase complex / epsilon DNA polymerase complex / DNA strand elongation involved in mitotic DNA replication / MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state ...establishment of sister chromatid cohesion / DNA-templated DNA replication maintenance of fidelity / Unwinding of DNA / DNA replication initiation / Cul8-RING ubiquitin ligase complex / epsilon DNA polymerase complex / DNA strand elongation involved in mitotic DNA replication / MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / nuclear DNA replication / MCM complex binding / GINS complex / mitotic DNA replication preinitiation complex assembly / premeiotic DNA replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / mitotic DNA replication / Activation of the pre-replicative complex / CMG complex / nuclear pre-replicative complex / Activation of ATR in response to replication stress / MCM complex / DNA replication preinitiation complex / double-strand break repair via break-induced replication / replication fork protection complex / mitotic DNA replication initiation / single-stranded DNA helicase activity / regulation of DNA-templated DNA replication initiation / silent mating-type cassette heterochromatin formation / DNA strand elongation involved in DNA replication / mitotic sister chromatid cohesion / nuclear chromosome / DNA unwinding involved in DNA replication / DNA replication origin binding / nuclear replication fork / subtelomeric heterochromatin formation / DNA replication initiation / error-prone translesion synthesis / heterochromatin formation / DNA helicase activity / helicase activity / DNA-templated DNA replication / nucleosome assembly / single-stranded DNA binding / mitotic cell cycle / DNA helicase / chromosome, telomeric region / hydrolase activity / cell cycle / DNA repair / chromatin binding / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast) | |||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.39 Å | |||||||||||||||||||||||||||
Authors | Dang S / Zhai Y / Feng J / Yu D | |||||||||||||||||||||||||||
Funding support | Hong Kong, 8 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Synergism between CMG helicase and leading strand DNA polymerase at replication fork. Authors: Zhichun Xu / Jianrong Feng / Daqi Yu / Yunjing Huo / Xiaohui Ma / Wai Hei Lam / Zheng Liu / Xiang David Li / Toyotaka Ishibashi / Shangyu Dang / Yuanliang Zhai / Abstract: The replisome that replicates the eukaryotic genome consists of at least three engines: the Cdc45-MCM-GINS (CMG) helicase that separates duplex DNA at the replication fork and two DNA polymerases, ...The replisome that replicates the eukaryotic genome consists of at least three engines: the Cdc45-MCM-GINS (CMG) helicase that separates duplex DNA at the replication fork and two DNA polymerases, one on each strand, that replicate the unwound DNA. Here, we determined a series of cryo-electron microscopy structures of a yeast replisome comprising CMG, leading-strand polymerase Polε and three accessory factors on a forked DNA. In these structures, Polε engages or disengages with the motor domains of the CMG by occupying two alternative positions, which closely correlate with the rotational movement of the single-stranded DNA around the MCM pore. During this process, the polymerase remains stably coupled to the helicase using Psf1 as a hinge. This synergism is modulated by a concerted rearrangement of ATPase sites to drive DNA translocation. The Polε-MCM coupling is not only required for CMG formation to initiate DNA replication but also facilitates the leading-strand DNA synthesis mediated by Polε. Our study elucidates a mechanism intrinsic to the replisome that coordinates the activities of CMG and Polε to negotiate any roadblocks, DNA damage, and epigenetic marks encountered during translocation along replication forks. | |||||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37345.map.gz | 306.6 MB | EMDB map data format | |
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Header (meta data) | emd-37345-v30.xml emd-37345.xml | 44.5 KB 44.5 KB | Display Display | EMDB header |
Images | emd_37345.png | 100 KB | ||
Masks | emd_37345_msk_1.map | 325 MB | Mask map | |
Filedesc metadata | emd-37345.cif.gz | 12.8 KB | ||
Others | emd_37345_half_map_1.map.gz emd_37345_half_map_2.map.gz | 301.9 MB 301.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37345 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37345 | HTTPS FTP |
-Related structure data
Related structure data | 8w7sMC 8kg6C 8kg8C 8kg9C 8w7mC C: citing same article (ref.) M: atomic model generated by this map |
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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_37345.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_37345_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_37345_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37345_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : replisome complex in state IV
+Supramolecule #1: replisome complex in state IV
+Macromolecule #1: DNA replication licensing factor MCM2
+Macromolecule #2: DNA replication licensing factor MCM3
+Macromolecule #3: DNA replication licensing factor MCM4
+Macromolecule #4: Minichromosome maintenance protein 5
+Macromolecule #5: DNA replication licensing factor MCM6
+Macromolecule #6: DNA replication licensing factor MCM7
+Macromolecule #7: DNA replication complex GINS protein PSF1
+Macromolecule #8: DNA replication complex GINS protein PSF2
+Macromolecule #9: DNA replication complex GINS protein PSF3
+Macromolecule #10: DNA replication complex GINS protein SLD5
+Macromolecule #11: Cell division control protein 45
+Macromolecule #12: DNA polymerase alpha-binding protein
+Macromolecule #14: DNA polymerase epsilon subunit B
+Macromolecule #13: DNA (71-mer)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: blot with filter paper for 3-4 seconds before plunging.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 4 / Number real images: 21776 / Average exposure time: 4.5 sec. / Average electron dose: 53.0 e/Å2 Details: Images were collected in movie-mode containing 40 frames. |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD Software: (Name: cryoSPARC (ver. v3.0.1), cryoSPARC (ver. v2.15.0)) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD Software: (Name: cryoSPARC (ver. v3.0.1), cryoSPARC (ver. v2.15.0)) |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: EXACT BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 7.39 Å / Resolution method: FSC 0.143 CUT-OFF Software: (Name: cryoSPARC (ver. v3.0.1), cryoSPARC (ver. v2.15.0)) Number images used: 7939 |