+Open data
-Basic information
Entry | Database: PDB / ID: 6s1n | ||||||
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Title | Human polymerase delta holoenzyme Conformer 2 | ||||||
Components |
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Keywords | REPLICATION / Protein | ||||||
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 / Cytosolic iron-sulfur cluster assembly / PCNA-p21 complex / 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 / Cytosolic iron-sulfur cluster assembly / 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 / Removal of the Flap Intermediate / 3'-5'-DNA exonuclease activity / 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 / aggresome / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / response to L-glutamate / histone acetyltransferase binding / DNA strand elongation involved in DNA replication / DNA biosynthetic process / error-free translesion synthesis / 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 / fatty acid homeostasis / mismatch repair / translesion synthesis / error-prone translesion synthesis / response to cadmium ion / DNA polymerase binding / response to UV / cyclin-dependent protein kinase holoenzyme complex / positive regulation of endothelial cell proliferation / 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 / cellular response to UV / cellular response to xenobiotic stimulus / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / heart development / protein-macromolecule adaptor activity / 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 / protein-containing complex binding / chromatin / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.86 Å | ||||||
Authors | Lancey, C. / Hamdan, S.M. / De Biasio, A. | ||||||
Funding support | United Kingdom, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6s1n.cif.gz | 465.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s1n.ent.gz | 362.6 KB | Display | PDB format |
PDBx/mmJSON format | 6s1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s1n_validation.pdf.gz | 533.3 KB | Display | wwPDB validaton report |
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Full document | 6s1n_full_validation.pdf.gz | 569.3 KB | Display | |
Data in XML | 6s1n_validation.xml.gz | 56.2 KB | Display | |
Data in CIF | 6s1n_validation.cif.gz | 91.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/6s1n ftp://data.pdbj.org/pub/pdb/validation_reports/s1/6s1n | HTTPS FTP |
-Related structure data
Related structure data | 10081MC 6s1mC 6s1oC 6tnyC 6tnzC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | |
EM raw data | EMPIAR-10824 (Title: Cryo electron micrographs of Pol delta-DNA-PCNA giving rise to various PCNA tilt angles Data size: 3.6 TB Data #1: Cryo-electron micrographs of Pol delta holoenzyme giving rise to different tilted conformers, collection 2 [micrographs - multiframe] Data #2: Cryo-electron micrographs of Pol delta holoenzyme giving rise to different tilted conformers, collection 1 [micrographs - multiframe] Data #3: Cryo-electron micrographs of Pol delta holoenzyme giving rise to different tilted conformers, collection 3 [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 4 molecules AEFG
#1: Protein | Mass: 123785.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLD1, POLD / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P28340, DNA-directed DNA polymerase, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters |
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#5: Protein | Mass: 29088.061 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12004 |
-DNA polymerase delta subunit ... , 3 types, 3 molecules BCD
#2: Protein | Mass: 51338.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLD2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P49005 |
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#3: Protein | Mass: 52528.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLD3, KIAA0039 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15054 |
#4: Protein | Mass: 16274.323 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLD4, POLDS / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9HCU8 |
-DNA chain , 2 types, 2 molecules PT
#6: DNA chain | Mass: 7665.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#7: DNA chain | Mass: 11677.539 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 3 molecules
#8: Chemical | ChemComp-ZN / |
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#9: Chemical | ChemComp-SF4 / |
#10: Chemical | ChemComp-TTP / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.355 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 130000 X / Nominal defocus max: 600 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 77 K |
Image recording | Average exposure time: 60 sec. / Electron dose: 35 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 3575 |
EM imaging optics | Phase plate: VOLTA PHASE PLATE |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||
3D reconstruction | Resolution: 4.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32282 / Symmetry type: POINT |