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Open data
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Basic information
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Title | Yeast replisome in state I | |||||||||||||||||||||||||||
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![]() | replisome / complex / DNA replication / REPLICATION | |||||||||||||||||||||||||||
Function / homology | ![]() establishment of sister chromatid cohesion / maintenance of DNA repeat elements / DNA-templated DNA replication maintenance of fidelity / gene conversion / Unwinding of DNA / replication fork arrest / Cul8-RING ubiquitin ligase complex / DNA replication initiation / meiotic chromosome segregation / epsilon DNA polymerase complex ...establishment of sister chromatid cohesion / maintenance of DNA repeat elements / DNA-templated DNA replication maintenance of fidelity / gene conversion / Unwinding of DNA / replication fork arrest / Cul8-RING ubiquitin ligase complex / DNA replication initiation / meiotic chromosome segregation / epsilon DNA polymerase complex / MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / MCM complex binding / GINS complex / DNA strand elongation involved in mitotic DNA replication / nuclear DNA replication / mitotic DNA replication preinitiation complex assembly / premeiotic DNA replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / mitotic DNA replication / SUMO binding / Activation of the pre-replicative complex / CMG complex / establishment of mitotic sister chromatid cohesion / DNA replication checkpoint signaling / nuclear pre-replicative complex / single-stranded DNA 3'-5' DNA exonuclease activity / MCM complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex / Termination of translesion DNA synthesis / mitotic DNA replication checkpoint signaling / replication fork protection complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / single-stranded DNA helicase activity / mitotic intra-S DNA damage checkpoint signaling / silent mating-type cassette heterochromatin formation / regulation of DNA-templated DNA replication initiation / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / mitotic sister chromatid cohesion / DNA replication proofreading / DNA strand elongation involved in DNA replication / nuclear chromosome / DNA unwinding involved in DNA replication / replication fork processing / leading strand elongation / nuclear replication fork / DNA replication origin binding / Dual incision in TC-NER / DNA replication initiation / subtelomeric heterochromatin formation / error-prone translesion synthesis / DNA helicase activity / base-excision repair, gap-filling / meiotic cell cycle / replication fork / helicase activity / transcription elongation by RNA polymerase II / base-excision repair / heterochromatin formation / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / double-strand break repair / nucleosome assembly / mitotic cell cycle / single-stranded DNA binding / 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 / DNA repair / nucleotide binding / mRNA binding / DNA damage response / chromatin binding / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.07 Å | |||||||||||||||||||||||||||
![]() | Dang S / Zhai Y / Feng J / Yu D / Xu Z | |||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 567.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 60.4 KB 60.4 KB | Display Display | ![]() |
Images | ![]() | 118.6 KB | ||
Masks | ![]() | 600.7 MB | ![]() | |
Filedesc metadata | ![]() | 16 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() | 300.4 MB 300.6 MB 300.3 MB 556.9 MB 556.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8kg6MC ![]() 8kg8C ![]() 8kg9C ![]() 8w7mC ![]() 8w7sC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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-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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-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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-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 | ||||||||||||
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-Half map: Half map1
File | emd_37211_half_map_1.map | ||||||||||||
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Annotation | Half map1 | ||||||||||||
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-Half map: Half map2
File | emd_37211_half_map_2.map | ||||||||||||
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Annotation | Half map2 | ||||||||||||
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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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![]() | single particle reconstruction |
Aggregation state | particle |
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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.. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
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. |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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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 |
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)) |