+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37211 | |||||||||||||||||||||||||||
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Title | Yeast replisome in state I | |||||||||||||||||||||||||||
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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 / gene conversion / maintenance of DNA repeat elements / Unwinding of DNA / replication fork arrest / DNA replication initiation / Cul8-RING ubiquitin ligase complex / meiotic chromosome segregation / epsilon DNA polymerase complex ...establishment of sister chromatid cohesion / DNA-templated DNA replication maintenance of fidelity / gene conversion / maintenance of DNA repeat elements / Unwinding of DNA / replication fork arrest / DNA replication initiation / Cul8-RING ubiquitin ligase complex / meiotic chromosome segregation / 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 / nucleotide-excision repair, DNA gap filling / SUMO binding / mitotic DNA replication / DNA replication proofreading / Activation of the pre-replicative complex / CMG complex / single-stranded DNA 3'-5' DNA exonuclease activity / establishment of mitotic sister chromatid cohesion / DNA replication checkpoint signaling / 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 / mitotic DNA replication checkpoint signaling / replication fork protection complex / mitotic DNA replication initiation / single-stranded DNA helicase activity / mitotic intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / silent mating-type cassette heterochromatin formation / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / mitotic sister chromatid cohesion / leading strand elongation / nuclear chromosome / DNA unwinding involved in DNA replication / replication fork processing / DNA replication origin binding / nuclear replication fork / subtelomeric heterochromatin formation / DNA replication initiation / error-prone translesion synthesis / heterochromatin formation / base-excision repair, gap-filling / DNA helicase activity / meiotic cell cycle / replication fork / helicase activity / base-excision repair / DNA-templated DNA replication / nucleosome assembly / double-strand break repair via nonhomologous end joining / double-strand break repair / single-stranded DNA binding / mitotic cell cycle / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / DNA helicase / DNA replication / chromosome, telomeric region / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / cell cycle / nucleotide binding / mRNA binding / DNA repair / DNA damage response / chromatin binding / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast) | |||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.07 Å | |||||||||||||||||||||||||||
Authors | Dang S / Zhai Y / Feng J / Yu D / Xu Z | |||||||||||||||||||||||||||
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_37211.map.gz | 567.3 MB | EMDB map data format | |
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Header (meta data) | emd-37211-v30.xml emd-37211.xml | 60.4 KB 60.4 KB | Display Display | EMDB header |
Images | emd_37211.png | 118.6 KB | ||
Masks | emd_37211_msk_1.map | 600.7 MB | Mask map | |
Filedesc metadata | emd-37211.cif.gz | 16 KB | ||
Others | emd_37211_additional_1.map.gz emd_37211_additional_2.map.gz emd_37211_additional_3.map.gz emd_37211_half_map_1.map.gz emd_37211_half_map_2.map.gz | 300.4 MB 300.6 MB 300.3 MB 556.9 MB 556.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37211 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37211 | HTTPS FTP |
-Related structure data
Related structure data | 8kg6MC 8kg8C 8kg9C 8w7mC 8w7sC 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_37211.map.gz / Format: CCP4 / Size: 600.7 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_37211_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: focused refined map for DPB2/Pol2 modelling
File | emd_37211_additional_1.map | ||||||||||||
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Annotation | focused refined map for DPB2/Pol2 modelling | ||||||||||||
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Density Histograms |
-Additional map: A map for Csm3/Tof1 modelling
File | emd_37211_additional_2.map | ||||||||||||
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Annotation | A map for Csm3/Tof1 modelling | ||||||||||||
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Density Histograms |
-Additional map: A map for the MCM5 WH domain modelling
File | emd_37211_additional_3.map | ||||||||||||
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Annotation | A map for the MCM5 WH domain modelling | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map1
File | emd_37211_half_map_1.map | ||||||||||||
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Annotation | Half map1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map2
File | emd_37211_half_map_2.map | ||||||||||||
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Annotation | Half map2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : replisome complex in state I
+Supramolecule #1: replisome complex in state I
+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 #15: Topoisomerase 1-associated factor 1
+Macromolecule #16: Chromosome segregation in meiosis protein 3
+Macromolecule #17: DNA polymerase epsilon catalytic subunit A
+Macromolecule #18: DNA polymerase epsilon subunit B
+Macromolecule #13: DNA (71-mer)
+Macromolecule #14: DNA (61-mer)
+Macromolecule #19: ZINC ION
+Macromolecule #20: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #21: MAGNESIUM ION
+Macromolecule #22: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | |||||||||||||||
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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: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF Software: (Name: cryoSPARC (ver. v3.0.1), cryoSPARC (ver. v2.15.0)) Number images used: 384519 |