+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4788 | |||||||||
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Title | D. melanogaster CMG-DNA with ATP, State 2B | |||||||||
Map data | State 2B, sharpened map (RELION PostProcess) | |||||||||
Sample |
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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 / Activation of the pre-replicative complex / eggshell chorion gene amplification / Orc1 removal from chromatin / DNA amplification / GINS complex ...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 / Activation of the pre-replicative complex / eggshell chorion gene amplification / Orc1 removal from chromatin / DNA amplification / GINS complex / DNA strand elongation involved in mitotic DNA replication / 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 / DNA duplex unwinding / DNA strand elongation involved in DNA replication / DNA unwinding involved in DNA replication / DNA replication origin binding / DNA replication initiation / meiotic cell cycle / DNA helicase activity / mitotic spindle organization / regulation of DNA-templated transcription elongation / helicase activity / mitotic cell cycle / single-stranded DNA binding / DNA replication / DNA helicase / cell division / chromatin binding / ATP hydrolysis activity / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.46 Å | |||||||||
Authors | Eickhoff P / Martino F / Locke J / Nans A / 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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4788.map.gz | 14.7 MB | EMDB map data format | |
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Header (meta data) | emd-4788-v30.xml emd-4788.xml | 36.1 KB 36.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4788_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_4788.png | 133.9 KB | ||
Others | emd_4788_additional.map.gz emd_4788_half_map_1.map.gz emd_4788_half_map_2.map.gz | 171.7 MB 171.2 MB 171.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4788 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4788 | HTTPS FTP |
-Validation report
Summary document | emd_4788_validation.pdf.gz | 435.9 KB | Display | EMDB validaton report |
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Full document | emd_4788_full_validation.pdf.gz | 435 KB | Display | |
Data in XML | emd_4788_validation.xml.gz | 19.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4788 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4788 | HTTPS FTP |
-Related structure data
Related structure data | 6razMC 4785C 4786C 4787C 6rawC 6raxC 6rayC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4788.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | State 2B, sharpened map (RELION PostProcess) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: State 2B, non-sharpened map (RELION Refine3D)
File | emd_4788_additional.map | ||||||||||||
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Annotation | State 2B, non-sharpened map (RELION Refine3D) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: State 2B, half-map 2 (RELION Refine3D)
File | emd_4788_half_map_1.map | ||||||||||||
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Annotation | State 2B, half-map 2 (RELION Refine3D) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: State 2B, half-map 1 (RELION Refine3D)
File | emd_4788_half_map_2.map | ||||||||||||
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Annotation | State 2B, half-map 1 (RELION Refine3D) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : CMG helicase bound to forked DNA in the presence of ATP, State 2B
+Supramolecule #1: CMG helicase bound to forked DNA in the presence of ATP, State 2B
+Supramolecule #2: CMG helicase
+Supramolecule #3: DNA
+Macromolecule #1: DNA
+Macromolecule #2: DNA
+Macromolecule #3: CDC45L
+Macromolecule #4: IP07275p
+Macromolecule #5: Probable DNA replication complex GINS protein PSF2
+Macromolecule #6: AT18545p
+Macromolecule #7: DNA replication complex GINS protein SLD5
+Macromolecule #8: DNA replication licensing factor Mcm2
+Macromolecule #9: DNA replication licensing factor Mcm5
+Macromolecule #10: DNA replication licensing factor Mcm6
+Macromolecule #11: DNA replication licensing factor Mcm3
+Macromolecule #12: DNA replication licensing factor MCM4
+Macromolecule #13: DNA replication licensing factor Mcm7
+Macromolecule #14: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #15: ADENOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |