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Open data
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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 / DNA strand elongation involved in mitotic DNA replication ...: / 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 / DNA strand elongation involved in mitotic DNA replication / GINS complex / MCM complex binding / mitotic DNA replication preinitiation complex assembly / nuclear DNA replication / premeiotic DNA replication / replication fork protection complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / SUMO binding / nucleotide-excision repair, DNA gap filling / Activation of the pre-replicative complex / mitotic DNA replication / CMG complex / nuclear pre-replicative complex / DNA replication proofreading / Termination of translesion DNA synthesis / DNA replication preinitiation complex / Activation of ATR in response to replication stress / single-stranded DNA 3'-5' DNA exonuclease activity / MCM complex / mitotic DNA replication checkpoint signaling / 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 / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / regulation of DNA-templated DNA replication initiation / mitotic sister chromatid cohesion / DNA strand elongation involved in DNA replication / 3'-5' DNA helicase activity / leading strand elongation / nuclear replication fork / DNA replication origin binding / Dual incision in TC-NER / DNA replication initiation / error-prone translesion synthesis / subtelomeric heterochromatin formation / base-excision repair, gap-filling / DNA helicase activity / replication fork / transcription elongation by RNA polymerase II / helicase activity / base-excision repair / double-strand break repair via nonhomologous end joining / DNA-templated DNA replication / heterochromatin formation / double-strand break repair / mitotic cell cycle / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / DNA helicase / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / chromosome, telomeric region / DNA replication / hydrolase activity / DNA repair / nucleotide binding / mRNA binding / DNA damage response / chromatin binding / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
| Biological species | ![]() | ||||||||||||
| 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: 2018Title: 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. | ||||||||||||
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Structure visualization
| Movie |
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| Structure viewer | EM map: SurfView Molmil Jmol/JSmol |
| Supplemental images |
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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 | 44.8 KB 44.8 KB | Display Display | EMDB header |
| Images | emd_0288.png | 92.5 KB | ||
| Filedesc metadata | emd-0288.cif.gz | 13.5 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 KB | Display | EMDB validaton report |
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| Full document | emd_0288_full_validation.pdf.gz | 425.5 KB | Display | |
| Data in XML | emd_0288_validation.xml.gz | 6.3 KB | Display | |
| Data in CIF | emd_0288_validation.cif.gz | 7.2 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 ( |
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| Similar structure data |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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
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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 |
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Sample preparation
| Buffer | pH: 7.6 |
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| Vitrification | Cryogen name: ETHANE |
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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 |
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Keywords
Authors
United Kingdom, 3 items
Citation
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