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Open data
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Basic information
| Entry | Database: PDB / ID: 8kg6 | |||||||||||||||||||||||||||
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| Title | Yeast replisome in state I | |||||||||||||||||||||||||||
Components |
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Keywords | REPLICATION / replisome / complex / DNA replication | |||||||||||||||||||||||||||
| Function / homology | Function and homology informationestablishment of sister chromatid cohesion / DNA-templated DNA replication maintenance of fidelity / gene conversion / Unwinding of DNA / maintenance of DNA repeat elements / DNA replication initiation / replication fork arrest / 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 / Unwinding of DNA / maintenance of DNA repeat elements / DNA replication initiation / replication fork arrest / Cul8-RING ubiquitin ligase complex / meiotic chromosome segregation / epsilon DNA polymerase complex / MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / DNA strand elongation involved in mitotic DNA replication / GINS complex / MCM complex binding / mitotic DNA replication preinitiation complex assembly / nuclear DNA replication / premeiotic DNA replication / replication fork protection complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / SUMO binding / nucleotide-excision repair, DNA gap filling / Activation of the pre-replicative complex / mitotic DNA replication / DNA replication checkpoint signaling / CMG complex / establishment of mitotic sister chromatid cohesion / nuclear pre-replicative complex / DNA replication proofreading / Termination of translesion DNA synthesis / Activation of ATR in response to replication stress / DNA replication preinitiation complex / single-stranded DNA 3'-5' DNA exonuclease activity / MCM complex / mitotic DNA replication checkpoint signaling / 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 / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / regulation of DNA-templated DNA replication initiation / mitotic sister chromatid cohesion / DNA strand elongation involved in DNA replication / nuclear chromosome / leading strand elongation / nuclear replication fork / replication fork processing / DNA replication origin binding / Dual incision in TC-NER / DNA replication initiation / error-prone translesion synthesis / subtelomeric heterochromatin formation / base-excision repair, gap-filling / DNA helicase activity / replication fork / meiotic cell cycle / transcription elongation by RNA polymerase II / helicase activity / base-excision repair / double-strand break repair via nonhomologous end joining / DNA-templated DNA replication / heterochromatin formation / double-strand break repair / mitotic cell cycle / nucleosome assembly / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / DNA helicase / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / chromosome, telomeric region / DNA replication / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||||||||
| Biological species | ![]() ![]() | |||||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å | |||||||||||||||||||||||||||
Authors | Dang, S. / Zhai, Y. / Feng, J. / Yu, D. / Xu, Z. | |||||||||||||||||||||||||||
| Funding support | Hong Kong, 8items
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Citation | Journal: Nat Commun / Year: 2023Title: 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
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 8kg6.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb8kg6.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 8kg6.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 8kg6_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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| Full document | 8kg6_full_validation.pdf.gz | 1.9 MB | Display | |
| Data in XML | 8kg6_validation.xml.gz | 224.3 KB | Display | |
| Data in CIF | 8kg6_validation.cif.gz | 347.4 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/8kg6 ftp://data.pdbj.org/pub/pdb/validation_reports/kg/8kg6 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 37211MC ![]() 8kg8C ![]() 8kg9C ![]() 8w7mC ![]() 8w7sC C: citing same article ( M: map data used to model this data |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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Components
-DNA replication licensing factor ... , 5 types, 5 molecules 23467
| #1: Protein | Mass: 98911.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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| #2: Protein | Mass: 107653.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
| #3: Protein | Mass: 105138.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
| #5: Protein | Mass: 113110.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
| #6: Protein | Mass: 95049.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein , 5 types, 7 molecules 5EFGHKL
| #4: Protein | Mass: 86505.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
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| #11: Protein | Mass: 74324.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
| #12: Protein | Mass: 104543.391 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #15: Protein | | Mass: 141296.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #16: Protein | | Mass: 36402.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-DNA replication complex GINS protein ... , 4 types, 4 molecules ABCD
| #7: Protein | Mass: 24230.576 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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| #8: Protein | Mass: 25096.807 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
| #9: Protein | Mass: 21977.135 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
| #10: Protein | Mass: 33983.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-DNA chain , 2 types, 2 molecules IJ
| #13: DNA chain | Mass: 22138.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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| #14: DNA chain | Mass: 18524.887 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-DNA polymerase epsilon ... , 2 types, 2 molecules MN
| #17: Protein | Mass: 255992.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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| #18: Protein | Mass: 78425.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 4 types, 17 molecules 






| #19: Chemical | ChemComp-ZN / #20: Chemical | #21: Chemical | ChemComp-MG / #22: Chemical | |
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-Details
| Has ligand of interest | Y |
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-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
| Component | Name: replisome complex in state I / Type: COMPLEX / Entity ID: #1-#18 / Source: RECOMBINANT | |||||||||||||||||||||||||
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| Molecular weight | Value: 1.70 MDa / Experimental value: NO | |||||||||||||||||||||||||
| Source (natural) | Organism: ![]() | |||||||||||||||||||||||||
| Source (recombinant) | Organism: ![]() | |||||||||||||||||||||||||
| Buffer solution | pH: 7.6 | |||||||||||||||||||||||||
| Buffer component |
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| Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
| Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 | |||||||||||||||||||||||||
| Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K Details: blot with filter paper for 3-4 seconds before plunging. |
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Electron microscopy imaging
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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| Microscopy | Model: FEI TITAN KRIOS |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
| Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
| Image recording | Average exposure time: 4.5 sec. / Electron dose: 53 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 4 / Num. of real images: 21776 Details: Images were collected in movie-mode containing 40 frames. |
| EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
| Image scans | Sampling size: 5 µm / Width: 5760 / Height: 4092 |
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Processing
| EM software |
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| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| 3D reconstruction | Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 384519 / Algorithm: EXACT BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Atomic model building | PDB-ID: 6XKL Accession code: 6XKL / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refine LS restraints |
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About Yorodumi






Hong Kong, 8items
Citation








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FIELD EMISSION GUN
