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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 / epsilon DNA polymerase complex / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity ...DNA replication initiation / epsilon DNA polymerase complex / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / 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) / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / 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 / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / histone acetyltransferase binding / DNA synthesis involved in DNA repair / DNA polymerase processivity factor activity / G1/S-Specific Transcription / response to dexamethasone / leading strand elongation / replication fork processing / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / Activation of the pre-replicative complex / PCNA-Dependent Long Patch Base Excision Repair / embryonic organ development / mismatch repair / translesion synthesis / cyclin-dependent protein kinase holoenzyme complex / response to cadmium ion / DNA polymerase binding / epithelial cell differentiation / positive regulation of DNA repair / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair, gap-filling / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of DNA replication / replication fork / male germ cell nucleus / 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 / DNA-templated DNA replication / receptor tyrosine kinase binding / cellular response to hydrogen peroxide / Dual incision in TC-NER / G1/S transition of mitotic cell cycle / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / mitotic cell cycle / 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 / chromatin / protein-containing complex binding / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / extracellular exosome / 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 epsilon. Authors: Roske JJ / Yeeles JTP | |||||||||
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 | 21.8 KB 21.8 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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Projections & Slices |
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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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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_50222_half_map_2.map | ||||||||||||
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Projections & Slices |
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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 |