+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0288 | ||||||||||||
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Title | S. cerevisiae CMG-Pol epsilon-DNA | ||||||||||||
Map data | CMG-Pol epsilon-DNA | ||||||||||||
Sample |
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Keywords | Helicase / Polymerase / DNA Replication / AAA+ protein / DNA BINDING PROTEIN | ||||||||||||
Function / homology | Function and homology information DNA-templated DNA replication maintenance of fidelity / gene conversion / Unwinding of DNA / DNA replication initiation / epsilon DNA polymerase complex / MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / MCM complex binding / GINS complex ...DNA-templated DNA replication maintenance of fidelity / gene conversion / Unwinding of DNA / DNA replication initiation / epsilon DNA polymerase complex / 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 / SUMO binding / Activation of the pre-replicative complex / CMG complex / nuclear pre-replicative complex / single-stranded DNA 3'-5' DNA exonuclease activity / MCM complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex / Termination of translesion DNA synthesis / mitotic DNA replication checkpoint signaling / replication fork protection complex / 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 / regulation of DNA-templated DNA replication initiation / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / mitotic sister chromatid cohesion / DNA replication proofreading / 3'-5' DNA helicase activity / DNA strand elongation involved in DNA replication / DNA unwinding involved in DNA replication / leading strand elongation / nuclear replication fork / DNA replication origin binding / Dual incision in TC-NER / DNA replication initiation / subtelomeric heterochromatin formation / error-prone translesion synthesis / DNA helicase activity / base-excision repair, gap-filling / replication fork / helicase activity / transcription elongation by RNA polymerase II / base-excision repair / heterochromatin formation / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / double-strand break repair / double-stranded DNA binding / mitotic cell cycle / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / chromosome, telomeric region / DNA replication / DNA helicase / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / hydrolase activity / DNA repair / chromatin binding / mRNA binding / nucleotide binding / DNA damage response / ATP hydrolysis activity / DNA binding / zinc ion binding / 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: 4.98 Å | ||||||||||||
Authors | Abid Ali F / Locke J / Nans A / Costa A | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structure of DNA-CMG-Pol epsilon elucidates the roles of the non-catalytic polymerase modules in the eukaryotic replisome. Authors: Panchali Goswami / Ferdos Abid Ali / Max E Douglas / Julia Locke / Andrew Purkiss / Agnieszka Janska / Patrik Eickhoff / Anne Early / Andrea Nans / Alan M C Cheung / John F X Diffley / Alessandro Costa / Abstract: Eukaryotic origin firing depends on assembly of the Cdc45-MCM-GINS (CMG) helicase. A key step is the recruitment of GINS that requires the leading-strand polymerase Pol epsilon, composed of Pol2, ...Eukaryotic origin firing depends on assembly of the Cdc45-MCM-GINS (CMG) helicase. A key step is the recruitment of GINS that requires the leading-strand polymerase Pol epsilon, composed of Pol2, Dpb2, Dpb3, Dpb4. While a truncation of the catalytic N-terminal Pol2 supports cell division, Dpb2 and C-terminal Pol2 (C-Pol2) are essential for viability. Dpb2 and C-Pol2 are non-catalytic modules, shown or predicted to be related to an exonuclease and DNA polymerase, respectively. Here, we present the cryo-EM structure of the isolated C-Pol2/Dpb2 heterodimer, revealing that C-Pol2 contains a DNA polymerase fold. We also present the structure of CMG/C-Pol2/Dpb2 on a DNA fork, and find that polymerase binding changes both the helicase structure and fork-junction engagement. Inter-subunit contacts that keep the helicase-polymerase complex together explain several cellular phenotypes. At least some of these contacts are preserved during Pol epsilon-dependent CMG assembly on path to origin firing, as observed with DNA replication reconstituted in vitro. | ||||||||||||
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_0288.map.gz | 38.9 MB | EMDB map data format | |
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Header (meta data) | emd-0288-v30.xml emd-0288.xml | 36 KB 36 KB | Display Display | EMDB header |
Images | emd_0288.png | 92.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0288 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0288 | HTTPS FTP |
-Validation report
Summary document | emd_0288_validation.pdf.gz | 426.3 KB | Display | EMDB validaton report |
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Full document | emd_0288_full_validation.pdf.gz | 425.9 KB | Display | |
Data in XML | emd_0288_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_0288_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0288 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0288 | HTTPS FTP |
-Related structure data
Related structure data | 6hv9MC 0287C 6hv8C 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_0288.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CMG-Pol epsilon-DNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.38 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-Pol epsilon-DNA
+Supramolecule #1: CMG-Pol epsilon-DNA
+Supramolecule #2: CMG-Pol epsilon
+Supramolecule #3: Nucleic acid
+Macromolecule #1: DNA replication licensing factor MCM3
+Macromolecule #2: DNA replication licensing factor MCM4
+Macromolecule #3: DNA replication licensing factor MCM5
+Macromolecule #4: DNA replication licensing factor MCM6
+Macromolecule #5: DNA replication licensing factor MCM2
+Macromolecule #6: DNA replication licensing factor MCM7
+Macromolecule #7: DNA replication complex GINS protein PSF1
+Macromolecule #8: DNA replication complex GINS protein PSF2
+Macromolecule #9: DNA replication complex GINS protein PSF3
+Macromolecule #10: DNA replication complex GINS protein SLD5
+Macromolecule #11: Cell division control protein 45
+Macromolecule #15: DNA polymerase epsilon subunit B
+Macromolecule #16: DNA polymerase epsilon catalytic subunit
+Macromolecule #12: DNA (5'-D(*GP*CP*AP*GP*CP*CP*AP*CP*GP*CP*TP*GP*GP*CP*CP*GP*TP*TP*...
+Macromolecule #13: DNA (5'-D(P*TP*AP*AP*AP*AP*CP*GP*GP*CP*CP*AP*GP*CP*GP*TP*GP*GP*CP...
+Macromolecule #14: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')
+Macromolecule #17: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
+Macromolecule #18: ZINC ION
-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) / Detector mode: COUNTING / Average electron dose: 4.2 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: EMDB MAP EMDB ID: |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Version: cryoSPARC / Number images used: 78556 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |