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Yorodumi- PDB-8ouw: Cryo-EM structure of CMG helicase bound to TIM-1/TIPN-1 and homod... -
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-Basic information
Entry | Database: PDB / ID: 8ouw | |||||||||
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Title | Cryo-EM structure of CMG helicase bound to TIM-1/TIPN-1 and homodimeric DNSN-1 on fork DNA (Caenorhabditis elegans) | |||||||||
Components |
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Keywords | REPLICATION / DNA Replication / DNA Replication Initiation / Replisome / DONSON | |||||||||
Function / homology | Function and homology information MCM complex assembly / Unwinding of DNA / Assembly of the pre-replicative complex / Orc1 removal from chromatin / Activation of the pre-replicative complex / Switching of origins to a post-replicative state / regulation of sister chromatid cohesion / : / replication fork arrest / gonad development ...MCM complex assembly / Unwinding of DNA / Assembly of the pre-replicative complex / Orc1 removal from chromatin / Activation of the pre-replicative complex / Switching of origins to a post-replicative state / regulation of sister chromatid cohesion / : / replication fork arrest / gonad development / cell cycle phase transition / DNA strand elongation involved in mitotic DNA replication / nuclear DNA replication / negative regulation of DNA helicase activity / GINS complex / mitotic DNA replication preinitiation complex assembly / meiotic sister chromatid cohesion / mitotic DNA replication / DNA replication checkpoint signaling / MCM complex / DNA replication preinitiation complex / double-strand break repair via break-induced replication / locomotion / replication fork protection complex / pronucleus / mitotic DNA replication initiation / mitotic intra-S DNA damage checkpoint signaling / embryo development ending in birth or egg hatching / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / mitotic sister chromatid cohesion / DNA duplex unwinding / DNA unwinding involved in DNA replication / replication fork processing / DNA replication origin binding / mitotic sister chromatid segregation / DNA replication initiation / condensed chromosome / DNA helicase activity / meiotic cell cycle / helicase activity / DNA-templated DNA replication / single-stranded DNA binding / chromosome / nervous system development / DNA helicase / DNA replication / hydrolase activity / cell cycle / cell division / DNA repair / chromatin binding / positive regulation of cell population proliferation / chromatin / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Caenorhabditis elegans (invertebrata) Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 Å | |||||||||
Authors | Jenkyn-Bedford, M. / Yeeles, J.T.P. / Labib, K.P.M. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Science / Year: 2023 Title: DNSN-1 recruits GINS for CMG helicase assembly during DNA replication initiation in . Authors: Yisui Xia / Remi Sonneville / Michael Jenkyn-Bedford / Liqin Ji / Constance Alabert / Ye Hong / Joseph T P Yeeles / Karim P M Labib / Abstract: Assembly of the CMG (CDC-45-MCM-2-7-GINS) helicase is the key regulated step during eukaryotic DNA replication initiation. Until now, it was unclear whether metazoa require additional factors that ...Assembly of the CMG (CDC-45-MCM-2-7-GINS) helicase is the key regulated step during eukaryotic DNA replication initiation. Until now, it was unclear whether metazoa require additional factors that are not present in yeast. In this work, we show that DNSN-1, the ortholog of human DONSON, functions during helicase assembly in a complex with MUS-101/TOPBP1. DNSN-1 is required to recruit the GINS complex to chromatin, and a cryo-electron microscopy structure indicates that DNSN-1 positions GINS on the MCM-2-7 helicase motor (comprising the six MCM-2 to MCM-7 proteins), by direct binding of DNSN-1 to GINS and MCM-3, using interfaces that we show are important for initiation and essential for viability. These findings identify DNSN-1 as a missing link in our understanding of DNA replication initiation, suggesting that initiation defects underlie the human disease syndrome that results from DONSON mutations. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ouw.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8ouw.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ouw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/8ouw ftp://data.pdbj.org/pub/pdb/validation_reports/ou/8ouw | HTTPS FTP |
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-Related structure data
Related structure data | 17204MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA replication licensing factor ... , 6 types, 6 molecules 234567
#1: Protein | Mass: 99448.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mcm-2, CELE_Y17G7B.5, Y17G7B.5 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q9XXI9, DNA helicase |
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#2: Protein | Mass: 90810.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mcm-3, C25D7.6, CELE_C25D7.6 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q9XVR7, DNA helicase |
#3: Protein | Mass: 91687.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mcm-4, let-358, lin-6, Y39G10AR.14 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q95XQ8, DNA helicase |
#4: Protein | Mass: 85057.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mcm-5, R10E4.4 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q21902, DNA helicase |
#5: Protein | Mass: 91248.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mcm-6, ZK632.1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P34647, DNA helicase |
#6: Protein | Mass: 81721.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mcm-7, MCM7, CELE_F32D1.10, F32D1.10 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O16297, DNA helicase |
-Probable DNA replication complex GINS protein ... , 2 types, 2 molecules AB
#7: Protein | Mass: 23064.361 Da / Num. of mol.: 1 Mutation: Protease-cleaved N-terminal expression tag (Gly-Pro-Gly-Ser) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: psf-1, R53.6 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q22019 |
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#8: Protein | Mass: 20349.330 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: psf-2, F31C3.5 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O62193 |
-DNA replication complex GINS protein ... , 2 types, 2 molecules CD
#9: Protein | Mass: 21717.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: psf-3, CELE_Y65B4BR.8, Y65B4BR.8 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q9BL54 |
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#10: Protein | Mass: 25705.123 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sld-5, CELE_Y113G7B.24, Y113G7B.24 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q9U2W9 |
-Protein , 4 types, 6 molecules EFGHKL
#11: Protein | Mass: 66245.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: evl-18, CELE_F34D10.2, F34D10.2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q7JMR0 | ||||
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#12: Protein | Mass: 66079.383 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: dnsn-1, C24H12.5, CELE_C24H12.5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H1ZUV7 #14: Protein | | Mass: 157256.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: tim-1, csg-5, Y75B8A.22 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G5EDN3 #15: Protein | | Mass: 27415.215 Da / Num. of mol.: 1 Mutation: Protease-cleaved N-terminal expression tag (Gly-Pro-Gly-Ser) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: tipn-1, F23C8.9 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q9TXI0 |
-DNA chain , 2 types, 3 molecules IJM
#13: DNA chain | Mass: 26396.836 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) #16: DNA chain | | Mass: 18524.887 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
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-Non-polymers , 3 types, 13 molecules
#17: Chemical | ChemComp-ZN / #18: Chemical | ChemComp-MG / #19: Chemical | ChemComp-ANP / |
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-Details
Has ligand of interest | N |
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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 |
-Sample preparation
Component | Name: Complex of CMG helicase bound to TIM-1/TIPN-1 and homodimeric DNSN-1 on fork DNA (Caenorhabditis elegans) Type: COMPLEX / Entity ID: #1-#16 / Source: RECOMBINANT |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 15 mA / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Cryogen name: ETHANE |
-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 FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Average exposure time: 1.7 sec. / Electron dose: 40.1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33900 / Symmetry type: POINT |