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Yorodumi- PDB-9f6l: Human DNA Polymerase epsilon bound to T-C mismatched DNA (Mismatc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9f6l | ||||||
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Title | Human DNA Polymerase epsilon bound to T-C mismatched DNA (Mismatch Excision state) | ||||||
Components |
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Keywords | REPLICATION / DNA / polymerase / epsilon / PCNA / leading strand / human / replisome / proofreading | ||||||
Function / homology | Function and homology information DNA replication initiation / epsilon DNA polymerase complex / single-stranded DNA 3'-5' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / DNA synthesis involved in DNA repair / leading strand elongation / Activation of the pre-replicative complex / PCNA-Dependent Long Patch Base Excision Repair ...DNA replication initiation / epsilon DNA polymerase complex / single-stranded DNA 3'-5' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / DNA synthesis involved in DNA repair / leading strand elongation / Activation of the pre-replicative complex / PCNA-Dependent Long Patch Base Excision Repair / embryonic organ development / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair, gap-filling / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / DNA-templated DNA replication / Dual incision in TC-NER / G1/S transition of mitotic cell cycle / Gap-filling DNA repair synthesis and ligation in TC-NER / mitotic cell cycle / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / chromatin binding / DNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Roske, J.J. / Yeeles, J.T.P. | ||||||
Funding support | United Kingdom, 1items
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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, J.J. / Yeeles, J.T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9f6l.cif.gz | 231.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9f6l.ent.gz | 176.4 KB | Display | PDB format |
PDBx/mmJSON format | 9f6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9f6l_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 9f6l_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 9f6l_validation.xml.gz | 41.7 KB | Display | |
Data in CIF | 9f6l_validation.cif.gz | 61.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/9f6l ftp://data.pdbj.org/pub/pdb/validation_reports/f6/9f6l | HTTPS FTP |
-Related structure data
Related structure data | 50228MC 9f6dC 9f6eC 9f6fC 9f6iC 9f6jC 9f6kC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 138239.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLE, POLE1 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q07864, DNA-directed DNA polymerase, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters | ||
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#2: DNA chain | Mass: 9489.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||
#3: DNA chain | Mass: 9458.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||
#4: Chemical | ChemComp-SF4 / | ||
#5: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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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 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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 defocus max: 3000 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 36.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.21_5207 / Category: model refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18858 / Symmetry type: POINT |
Refinement | Cross valid method: NONE |