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Yorodumi- EMDB-50222: Human DNA polymerase epsilon bound to DNA and PCNA (open conformation) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50222 | |||||||||
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Title | Human DNA polymerase epsilon bound to DNA and PCNA (open conformation) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DNA / polymerase / epsilon / PCNA / leading strand / human / replication / replisome / proofreading | |||||||||
Function / homology | Function and homology information DNA replication initiation / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / epsilon DNA polymerase complex / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / MutLalpha complex binding / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity ...DNA replication initiation / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / epsilon DNA polymerase complex / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / MutLalpha complex binding / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / nucleotide-excision repair, DNA gap filling / single-stranded DNA 3'-5' DNA exonuclease activity / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Polymerase switching on the C-strand of the telomere / DNA replication proofreading / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / replisome / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / response to L-glutamate / histone acetyltransferase binding / DNA synthesis involved in DNA repair / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / replication fork processing / response to dexamethasone / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / mismatch repair / embryonic organ development / translesion synthesis / response to cadmium ion / DNA polymerase binding / cyclin-dependent protein kinase holoenzyme complex / epithelial cell differentiation / base-excision repair, gap-filling / positive regulation of DNA repair / Translesion synthesis by REV1 / Translesion synthesis by POLK / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of DNA replication / male germ cell nucleus / replication fork / liver regeneration / nuclear estrogen receptor binding / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / receptor tyrosine kinase binding / DNA-templated DNA replication / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / G1/S transition of mitotic cell cycle / cellular response to UV / cellular response to xenobiotic stimulus / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / mitotic cell cycle / heart development / 4 iron, 4 sulfur cluster binding / DNA replication / damaged DNA binding / chromosome, telomeric region / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear body / nucleotide binding / centrosome / chromatin binding / protein-containing complex binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Roske JJ / Yeeles JTP | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol ε. Authors: Johann J Roske / Joseph T P Yeeles / Abstract: During chromosome replication, the nascent leading strand is synthesized by DNA polymerase epsilon (Pol ε), which associates with the sliding clamp processivity factor proliferating cell nuclear ...During chromosome replication, the nascent leading strand is synthesized by DNA polymerase epsilon (Pol ε), which associates with the sliding clamp processivity factor proliferating cell nuclear antigen (PCNA) to form a processive holoenzyme. For high-fidelity DNA synthesis, Pol ε relies on nucleotide selectivity and its proofreading ability to detect and excise a misincorporated nucleotide. Here, we present cryo-electron microscopy (cryo-EM) structures of human Pol ε in complex with PCNA, DNA and an incoming nucleotide, revealing how Pol ε associates with PCNA through its PCNA-interacting peptide box and additional unique features of its catalytic domain. Furthermore, by solving a series of cryo-EM structures of Pol ε at a mismatch-containing DNA, we elucidate how Pol ε senses and edits a misincorporated nucleotide. Our structures delineate steps along an intramolecular switching mechanism between polymerase and exonuclease activities, providing the basis for a proofreading mechanism in B-family replicative polymerases. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_50222.map.gz | 223.6 MB | EMDB map data format | |
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Header (meta data) | emd-50222-v30.xml emd-50222.xml | 21.9 KB 21.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_50222_fsc.xml | 14.9 KB | Display | FSC data file |
Images | emd_50222.png | 131.6 KB | ||
Masks | emd_50222_msk_1.map emd_50222_msk_2.map | 236.9 MB 236.9 MB | Mask map | |
Filedesc metadata | emd-50222.cif.gz | 7 KB | ||
Others | emd_50222_additional_1.map.gz emd_50222_half_map_1.map.gz emd_50222_half_map_2.map.gz | 223.6 MB 219.8 MB 219.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50222 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50222 | HTTPS FTP |
-Validation report
Summary document | emd_50222_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_50222_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_50222_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | emd_50222_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50222 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50222 | HTTPS FTP |
-Related structure data
Related structure data | 9f6dMC 9f6eC 9f6fC 9f6iC 9f6jC 9f6kC 9f6lC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_50222.map.gz / Format: CCP4 / Size: 236.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84065 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_50222_msk_1.map | ||||||||||||
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Density Histograms |
-Mask #2
File | emd_50222_msk_2.map | ||||||||||||
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Density Histograms |
-Additional map: Map from focussed refinement with Mask around Polymerase...
File | emd_50222_additional_1.map | ||||||||||||
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Annotation | Map from focussed refinement with Mask around Polymerase epsilon catalytic domain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_50222_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_50222_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
+Entire : Quaternary Complex of human leading strand polymerase epsilon, Pr...
+Supramolecule #1: Quaternary Complex of human leading strand polymerase epsilon, Pr...
+Supramolecule #2: DNA polymerase epsilon catalytic subunit A
+Supramolecule #3: Proliferating cell nuclear antigen
+Supramolecule #4: DNA
+Macromolecule #1: DNA polymerase epsilon catalytic subunit A
+Macromolecule #2: Proliferating cell nuclear antigen
+Macromolecule #3: DNA nascent strand
+Macromolecule #4: DNA template strand
+Macromolecule #5: IRON/SULFUR CLUSTER
+Macromolecule #6: 2',3'-dideoxyadenosine triphosphate
+Macromolecule #7: MAGNESIUM ION
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.08 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |