+Open data
-Basic information
Entry | Database: PDB / ID: 6ray | ||||||
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Title | D. melanogaster CMG-DNA, State 2A | ||||||
Components |
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Keywords | REPLICATION / Helicase / ATPase / AAA+ / DNA unwinding | ||||||
Function / homology | Function and homology information Unwinding of DNA / Switching of origins to a post-replicative state / Assembly of the pre-replicative complex / DNA endoreduplication / Activation of ATR in response to replication stress / single-stranded 3'-5' DNA helicase activity / Activation of the pre-replicative complex / eggshell chorion gene amplification / Orc1 removal from chromatin / DNA amplification ...Unwinding of DNA / Switching of origins to a post-replicative state / Assembly of the pre-replicative complex / DNA endoreduplication / Activation of ATR in response to replication stress / single-stranded 3'-5' DNA helicase activity / Activation of the pre-replicative complex / eggshell chorion gene amplification / Orc1 removal from chromatin / DNA amplification / DNA strand elongation involved in mitotic DNA replication / GINS complex / mitotic DNA replication preinitiation complex assembly / resolution of meiotic recombination intermediates / premeiotic DNA replication / mitotic DNA replication / CMG complex / MCM complex / DNA replication preinitiation complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / chromosome condensation / single-stranded DNA helicase activity / DNA strand elongation involved in DNA replication / 3'-5' DNA helicase activity / DNA unwinding involved in DNA replication / DNA replication origin binding / DNA replication initiation / mitotic spindle organization / meiotic cell cycle / regulation of DNA-templated transcription elongation / mitotic cell cycle / single-stranded DNA binding / DNA helicase / DNA replication / cell division / chromatin binding / ATP hydrolysis activity / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.28 Å | ||||||
Authors | Eickhoff, P. / Martino, F. / Costa, A. | ||||||
Citation | Journal: Cell Rep / Year: 2019 Title: Molecular Basis for ATP-Hydrolysis-Driven DNA Translocation by the CMG Helicase of the Eukaryotic Replisome. Authors: Patrik Eickhoff / Hazal B Kose / Fabrizio Martino / Tatjana Petojevic / Ferdos Abid Ali / Julia Locke / Nele Tamberg / Andrea Nans / James M Berger / Michael R Botchan / Hasan Yardimci / Alessandro Costa / Abstract: In the eukaryotic replisome, DNA unwinding by the Cdc45-MCM-Go-Ichi-Ni-San (GINS) (CMG) helicase requires a hexameric ring-shaped ATPase named minichromosome maintenance (MCM), which spools single- ...In the eukaryotic replisome, DNA unwinding by the Cdc45-MCM-Go-Ichi-Ni-San (GINS) (CMG) helicase requires a hexameric ring-shaped ATPase named minichromosome maintenance (MCM), which spools single-stranded DNA through its central channel. Not all six ATPase sites are required for unwinding; however, the helicase mechanism is unknown. We imaged ATP-hydrolysis-driven translocation of the CMG using cryo-electron microscopy (cryo-EM) and found that the six MCM subunits engage DNA using four neighboring protomers at a time, with ATP binding promoting DNA engagement. Morphing between different helicase states leads us to suggest a non-symmetric hand-over-hand rotary mechanism, explaining the asymmetric requirements of ATPase function around the MCM ring of the CMG. By imaging of a higher-order replisome assembly, we find that the Mrc1-Csm3-Tof1 fork-stabilization complex strengthens the interaction between parental duplex DNA and the CMG at the fork, which might support the coupling between DNA translocation and fork unwinding. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ray.cif.gz | 893.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ray.ent.gz | 727.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ray.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/6ray ftp://data.pdbj.org/pub/pdb/validation_reports/ra/6ray | HTTPS FTP |
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-Related structure data
Related structure data | 4787MC 4785C 4786C 4788C 6rawC 6raxC 6razC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA replication licensing factor ... , 6 types, 6 molecules 347652
#1: Protein | Mass: 91045.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Mcm3, Mcm3-RA, CG4206 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9XYU1, DNA helicase |
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#2: Protein | Mass: 96735.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dpa, CG1616 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q26454, DNA helicase |
#3: Protein | Mass: 81399.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Mcm7, CG4978 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9XYU0, DNA helicase |
#4: Protein | Mass: 92467.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Mcm6, CG4039 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9V461, DNA helicase |
#5: Protein | Mass: 82375.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Mcm5, CG4082 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9VGW6, DNA helicase |
#11: Protein | Mass: 100537.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Mcm2, CG7538 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P49735, DNA helicase |
-Protein , 5 types, 5 molecules AHLMN
#6: Protein | Mass: 65968.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: CDC45L, anon-1Ec, CDC45, Cdc45, cdc45, D, dCDC45, dCDC45L, DmCdc45, Dmel\CG3658, EG:BACR7A4.11, CG3658, Dmel_CG3658 Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O96989 |
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#7: Protein | Mass: 23333.693 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: Psf1, CG9187-PA, Dmel\CG9187, psf1, CG9187, Dmel_CG9187 Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9W0I7 |
#8: Protein | Mass: 23141.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Psf2, CG18013 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9VQY9 |
#9: Protein | Mass: 24829.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Psf3, Dmel\CG2222, CG2222, Dmel_CG2222 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9W2V7 |
#10: Protein | Mass: 26148.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: Sld5, anon-WO0172774.61, Dmel\CG14549, CG14549, Dmel_CG14549 Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9VBI1 |
-DNA chain , 1 types, 1 molecules X
#12: DNA chain | Mass: 3918.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) |
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-Non-polymers , 2 types, 6 molecules
#13: Chemical | ChemComp-ATP / #14: 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 |
-Sample preparation
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Source (recombinant) |
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Buffer solution | pH: 7.6 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
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: OTHER |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52214 / Symmetry type: POINT |