+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10539 | |||||||||
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Title | Processive human polymerase delta holoenzyme | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Protein / REPLICATION | |||||||||
Function / homology | Function and homology information delta DNA polymerase complex / DNA synthesis involved in UV-damage excision repair / nucleotide-excision repair complex / zeta DNA polymerase complex / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / Cytosolic iron-sulfur cluster assembly / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity ...delta DNA polymerase complex / DNA synthesis involved in UV-damage excision repair / nucleotide-excision repair complex / zeta DNA polymerase complex / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / Cytosolic iron-sulfur cluster assembly / 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 / 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 / aggresome / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / response to L-glutamate / nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA replication proofreading / DNA strand elongation involved in DNA replication / histone acetyltransferase binding / error-free translesion synthesis / DNA biosynthetic process / 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 / PCNA-Dependent Long Patch Base Excision Repair / fatty acid homeostasis / mismatch repair / error-prone translesion synthesis / translesion synthesis / cyclin-dependent protein kinase holoenzyme complex / response to cadmium ion / DNA polymerase binding / response to UV / positive regulation of endothelial cell proliferation / 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 / 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 / protein-macromolecule adaptor activity / 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 / DNA repair / nucleotide binding / centrosome / chromatin binding / chromatin / protein-containing complex binding / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.08 Å | |||||||||
Authors | Lancey C / Hamdan SM | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structure of the processive human Pol δ holoenzyme. Authors: Claudia Lancey / Muhammad Tehseen / Vlad-Stefan Raducanu / Fahad Rashid / Nekane Merino / Timothy J Ragan / Christos G Savva / Manal S Zaher / Afnan Shirbini / Francisco J Blanco / Samir M ...Authors: Claudia Lancey / Muhammad Tehseen / Vlad-Stefan Raducanu / Fahad Rashid / Nekane Merino / Timothy J Ragan / Christos G Savva / Manal S Zaher / Afnan Shirbini / Francisco J Blanco / Samir M Hamdan / Alfredo De Biasio / Abstract: In eukaryotes, DNA polymerase δ (Pol δ) bound to the proliferating cell nuclear antigen (PCNA) replicates the lagging strand and cooperates with flap endonuclease 1 (FEN1) to process the Okazaki ...In eukaryotes, DNA polymerase δ (Pol δ) bound to the proliferating cell nuclear antigen (PCNA) replicates the lagging strand and cooperates with flap endonuclease 1 (FEN1) to process the Okazaki fragments for their ligation. We present the high-resolution cryo-EM structure of the human processive Pol δ-DNA-PCNA complex in the absence and presence of FEN1. Pol δ is anchored to one of the three PCNA monomers through the C-terminal domain of the catalytic subunit. The catalytic core sits on top of PCNA in an open configuration while the regulatory subunits project laterally. This arrangement allows PCNA to thread and stabilize the DNA exiting the catalytic cleft and recruit FEN1 to one unoccupied monomer in a toolbelt fashion. Alternative holoenzyme conformations reveal important functional interactions that maintain PCNA orientation during synthesis. This work sheds light on the structural basis of Pol δ's activity in replicating the human genome. | |||||||||
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_10539.map.gz | 15.3 MB | EMDB map data format | |
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Header (meta data) | emd-10539-v30.xml emd-10539.xml | 25.3 KB 25.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10539_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_10539.png | 58.4 KB | ||
Filedesc metadata | emd-10539.cif.gz | 8.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10539 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10539 | HTTPS FTP |
-Validation report
Summary document | emd_10539_validation.pdf.gz | 189.9 KB | Display | EMDB validaton report |
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Full document | emd_10539_full_validation.pdf.gz | 189.5 KB | Display | |
Data in XML | emd_10539_validation.xml.gz | 503 B | Display | |
Data in CIF | emd_10539_validation.cif.gz | 374 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10539 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10539 | HTTPS FTP |
-Related structure data
Related structure data | 6tnyMC 6s1mC 6s1nC 6s1oC 6tnzC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10823 (Title: Cryo electron micrographs of Pol delta-PCNA-DNA-FEN1 sample Data size: 1.6 TB Data #1: Cryo-electron micrographs of Pol delta-FEN1 toolbelt [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10539.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.87 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 : Toolbelt
+Supramolecule #1: Toolbelt
+Supramolecule #2: DNA polymerase
+Supramolecule #3: Proliferating cell nuclear antigen
+Supramolecule #4: DNA primer, template
+Macromolecule #1: DNA polymerase delta catalytic subunit
+Macromolecule #2: DNA polymerase delta subunit 2
+Macromolecule #3: DNA polymerase delta subunit 3
+Macromolecule #4: DNA polymerase delta subunit 4
+Macromolecule #5: Proliferating cell nuclear antigen
+Macromolecule #6: DNA primer
+Macromolecule #7: DNA template
+Macromolecule #8: ZINC ION
+Macromolecule #9: IRON/SULFUR CLUSTER
+Macromolecule #10: THYMIDINE-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 Component:
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Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 300 sec. | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||||||||
Details | Complex separated by gel filtration |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 77.0 K / Max: 77.0 K |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Number real images: 5071 / Average exposure time: 3.0 sec. / Average electron dose: 44.0 e/Å2 / Details: Data were collected in super resolution mode |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 57471 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |