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Yorodumi- EMDB-20607: Structure of the S. cerevisiae replicative helicase CMG in comple... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20607 | ||||||||||||
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Title | Structure of the S. cerevisiae replicative helicase CMG in complex with a forked DNA | ||||||||||||
Map data | eukaryotic replicative CMG helicase | ||||||||||||
Sample |
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Keywords | DNA replication / CMG-Mcm10 / REPLICATION-DNA complex | ||||||||||||
Function / homology | Function and homology information Unwinding of DNA / 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 ...Unwinding of DNA / 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 / Activation of the pre-replicative complex / CMG complex / single-stranded 3'-5' DNA helicase activity / nuclear pre-replicative complex / MCM complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex / replication fork protection complex / mitotic DNA replication initiation / double-strand break repair via break-induced replication / silent mating-type cassette heterochromatin formation / regulation of DNA-templated DNA replication initiation / single-stranded DNA helicase activity / DNA strand elongation involved in DNA replication / DNA unwinding involved in DNA replication / nuclear replication fork / 3'-5' DNA helicase activity / DNA replication origin binding / subtelomeric heterochromatin formation / DNA replication initiation / helicase activity / heterochromatin formation / DNA-templated DNA replication / single-stranded DNA binding / DNA helicase / chromosome, telomeric region / DNA damage response / chromatin binding / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Yuan Z / Georgescu R | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nat Commun / Year: 2020 Title: DNA unwinding mechanism of a eukaryotic replicative CMG helicase. Authors: Zuanning Yuan / Roxana Georgescu / Lin Bai / Dan Zhang / Huilin Li / Michael E O'Donnell / Abstract: High-resolution structures have not been reported for replicative helicases at a replication fork at atomic resolution, a prerequisite to understanding the unwinding mechanism. The eukaryotic ...High-resolution structures have not been reported for replicative helicases at a replication fork at atomic resolution, a prerequisite to understanding the unwinding mechanism. The eukaryotic replicative CMG (Cdc45, Mcm2-7, GINS) helicase contains a Mcm2-7 motor ring, with the N-tier ring in front and the C-tier motor ring behind. The N-tier ring is structurally divided into a zinc finger (ZF) sub-ring followed by the oligosaccharide/oligonucleotide-binding (OB) fold ring. Here we report the cryo-EM structure of CMG on forked DNA at 3.9 Å, revealing that parental DNA enters the ZF sub-ring and strand separation occurs at the bottom of the ZF sub-ring, where the lagging strand is blocked and diverted sideways by OB hairpin-loops of Mcm3, Mcm4, Mcm6, and Mcm7. Thus, instead of employing a specific steric exclusion process, or even a separation pin, unwinding is achieved via a "dam-and-diversion tunnel" mechanism that does not require specific protein-DNA interaction. The C-tier motor ring contains spirally configured PS1 and H2I loops of Mcms 2, 3, 5, 6 that translocate on the spirally-configured leading strand, and thereby pull the preceding DNA segment through the diversion tunnel for strand separation. | ||||||||||||
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_20607.map.gz | 9.3 MB | EMDB map data format | |
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Header (meta data) | emd-20607-v30.xml emd-20607.xml | 28.2 KB 28.2 KB | Display Display | EMDB header |
Images | emd_20607.png | 137.1 KB | ||
Filedesc metadata | emd-20607.cif.gz | 9.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20607 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20607 | HTTPS FTP |
-Validation report
Summary document | emd_20607_validation.pdf.gz | 434.2 KB | Display | EMDB validaton report |
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Full document | emd_20607_full_validation.pdf.gz | 433.7 KB | Display | |
Data in XML | emd_20607_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_20607_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20607 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20607 | HTTPS FTP |
-Related structure data
Related structure data | 6u0mMC 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_20607.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | eukaryotic replicative CMG helicase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.074 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : CMG-forkDNA
+Supramolecule #1: CMG-forkDNA
+Macromolecule #1: DNA replication complex GINS protein PSF1
+Macromolecule #2: DNA replication complex GINS protein PSF2
+Macromolecule #3: DNA replication complex GINS protein PSF3
+Macromolecule #4: DNA replication complex GINS protein SLD5
+Macromolecule #5: Cell division control protein 45
+Macromolecule #6: DNA replication licensing factor MCM2
+Macromolecule #7: DNA replication licensing factor MCM3
+Macromolecule #8: DNA replication licensing factor MCM4
+Macromolecule #9: Minichromosome maintenance protein 5
+Macromolecule #10: DNA replication licensing factor MCM6
+Macromolecule #11: DNA replication licensing factor MCM7
+Macromolecule #12: DNA (26-MER)
+Macromolecule #13: DNA (15-MER)
+Macromolecule #14: 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: 7.5 |
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Grid | Details: unspecified |
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) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 162550 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-6u0m: |