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- PDB-8yjz: Structure of the human endogenous PCNA-FEN1-RNase H2 complex - State D -
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Basic information
Entry | Database: PDB / ID: 8yjz | ||||||
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Title | Structure of the human endogenous PCNA-FEN1-RNase H2 complex - State D | ||||||
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![]() | DNA BINDING PROTEIN/DNA / Flap endonuclease 1 / RNase H2 / endogenous DNA / PCNA / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() ribonucleotide metabolic process / ribonuclease H2 complex / flap endonuclease activity / positive regulation of sister chromatid cohesion / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication ...ribonucleotide metabolic process / ribonuclease H2 complex / flap endonuclease activity / positive regulation of sister chromatid cohesion / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / 5'-flap endonuclease activity / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / UV protection / Polymerase switching / MutLalpha complex binding / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / regulation of DNA damage checkpoint / PCNA complex / DNA replication, removal of RNA primer / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / HDR through MMEJ (alt-NHEJ) / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / Transcription of E2F targets under negative control by DREAM complex / RNA catabolic process / replisome / 5'-3' exonuclease activity / exonuclease activity / ribonuclease H / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / leading strand elongation / Early Phase of HIV Life Cycle / G1/S-Specific Transcription / response to dexamethasone / replication fork processing / nuclear replication fork / SUMOylation of DNA replication proteins / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / RNA nuclease activity / mismatch repair / translesion synthesis / response to cadmium ion / estrous cycle / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / regulation of G2/M transition of mitotic cell cycle / DNA polymerase binding / epithelial cell differentiation / positive regulation of DNA repair / male germ cell nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by REV1 / Translesion synthesis by POLK / liver regeneration / replication fork / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of DNA replication / nuclear estrogen receptor binding / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / double-strand break repair via homologous recombination / Translesion Synthesis by POLH / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / memory / Dual Incision in GG-NER / cellular response to hydrogen peroxide / positive regulation of fibroblast proliferation / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA-DNA hybrid ribonuclease activity / cellular response to UV / cellular response to xenobiotic stimulus / double-strand break repair / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / manganese ion binding / heart development / double-stranded DNA binding / fibroblast proliferation / endonuclease activity / gene expression / in utero embryonic development / damaged DNA binding / Hydrolases; Acting on ester bonds / chromosome, telomeric region / DNA replication / nuclear body / negative regulation of gene expression / DNA repair Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.15 Å | ||||||
![]() | Tian, Y. / Gao, N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insight into Okazaki fragment maturation mediated by PCNA-bound FEN1 and RNaseH2. Authors: Yuhui Tian / Ningning Li / Qing Li / Ning Gao / ![]() Abstract: PCNA is a master coordinator of many DNA-metabolic events. During DNA replication, the maturation of Okazaki fragments involves at least four DNA enzymes, all of which contain PCNA-interacting motifs. ...PCNA is a master coordinator of many DNA-metabolic events. During DNA replication, the maturation of Okazaki fragments involves at least four DNA enzymes, all of which contain PCNA-interacting motifs. However, the temporal relationships and functional modulations between these PCNA-binding proteins are unclear. Here, we developed a strategy to purify endogenous PCNA-containing complexes from native chromatin, and characterized their structures using cryo-EM. Two structurally resolved classes (PCNA-FEN1 and PCNA-FEN1-RNaseH2 complexes) have captured a series of 3D snapshots for the primer-removal steps of Okazaki fragment maturation. These structures show that product release from FEN1 is a rate-liming step. Furthermore, both FEN1 and RNaseH2 undergo continuous conformational changes on PCNA that result in constant fluctuations in the bending angle of substrate DNA at the nick site, implying that these enzymes could regulate each other through conformational modulation of the bound DNA. The structures of the PCNA-FEN1-RNaseH2 complex confirm the toolbelt function of PCNA and suggests a potential unrecognized role of RNaseH2, as a dsDNA binding protein, in promoting the 5'-flap cleaving activity of FEN1. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 344.5 KB | Display | ![]() |
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PDB format | ![]() | 273.5 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 409.6 KB | Display | ![]() |
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Full document | ![]() | 426.1 KB | Display | |
Data in XML | ![]() | 34.6 KB | Display | |
Data in CIF | ![]() | 53.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 39354MC ![]() 8yjhC ![]() 8yjlC ![]() 8yjqC ![]() 8yjrC ![]() 8yjsC ![]() 8yjuC ![]() 8yjvC ![]() 8yjwC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 2 types, 4 molecules BCAD
#1: Protein | Mass: 28795.752 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | | Mass: 42661.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P39748, Hydrolases; Acting on ester bonds |
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-Ribonuclease H2 subunit ... , 3 types, 3 molecules HGI
#3: Protein | Mass: 33431.844 Da / Num. of mol.: 1 / Fragment: subunit A / Source method: isolated from a natural source / Source: (natural) ![]() |
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#4: Protein | Mass: 35195.727 Da / Num. of mol.: 1 / Fragment: subunit B / Source method: isolated from a natural source / Source: (natural) ![]() |
#5: Protein | Mass: 17862.137 Da / Num. of mol.: 1 / Fragment: subunit C / Source method: isolated from a natural source / Source: (natural) ![]() |
-DNA chain , 3 types, 3 molecules JEF
#6: DNA chain | Mass: 6101.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#7: DNA chain | Mass: 9565.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#8: DNA chain | Mass: 4249.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Details
Has protein modification | 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 |
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Sample preparation
Component | Name: endogenous state D PCNA-DNA-FEN1-RNase H2 complex / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 2000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 5.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13906 / Symmetry type: POINT | ||||||||||||||||||||||||
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