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Yorodumi- EMDB-6339: Molecular architecture of the Ub-PCNA/Pol eta complex bound to DNA -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6339 | |||||||||
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Title | Molecular architecture of the Ub-PCNA/Pol eta complex bound to DNA | |||||||||
Map data | Reconstruction of Ub-PCNA/Pol eta/DNA ternary complex | |||||||||
Sample |
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Keywords | Translesion synthesis / DNA damage tolerance / Y-Family polymerase / PCNA monoubiquitination | |||||||||
Function / homology | Function and homology information 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 ...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 / 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 / response to UV-C / response to L-glutamate / histone acetyltransferase binding / DNA synthesis involved in DNA repair / error-free translesion synthesis / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / response to dexamethasone / replication fork processing / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / 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 / response to radiation / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / 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 / site of double-strand break / heart development / DNA replication / chromosome, telomeric region / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear body / DNA repair / centrosome / chromatin binding / protein-containing complex binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 22.0 Å | |||||||||
Authors | Lau WCY / Li Y / Zhang Q / Huen MSY | |||||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Molecular architecture of the Ub-PCNA/Pol η complex bound to DNA. Authors: Wilson C Y Lau / Yinyin Li / Qinfen Zhang / Michael S Y Huen / Abstract: Translesion synthesis (TLS) is the mechanism by which DNA polymerases replicate through unrepaired DNA lesions. TLS is activated by monoubiquitination of the homotrimeric proliferating cell nuclear ...Translesion synthesis (TLS) is the mechanism by which DNA polymerases replicate through unrepaired DNA lesions. TLS is activated by monoubiquitination of the homotrimeric proliferating cell nuclear antigen (PCNA) at lysine-164, followed by the switch from replicative to specialized polymerases at DNA damage sites. Pol η belongs to the Y-Family of specialized polymerases that can efficiently bypass UV-induced lesions. Like other members of the Y-Family polymerases, its recruitment to the damaged sites is mediated by the interaction with monoubiquitinated PCNA (Ub-PCNA) via its ubiquitin-binding domain and non-canonical PCNA-interacting motif in the C-terminal region. The structural determinants underlying the direct recognition of Ub-PCNA by Pol η, or Y-Family polymerases in general, remain largely unknown. Here we report a structure of the Ub-PCNA/Pol η complex bound to DNA determined by single-particle electron microscopy (EM). The overall obtained structure resembles that of the editing PCNA/PolB complex. Analysis of the map revealed the conformation of ubiquitin that binds the C-terminal domain of Pol η. Our present study suggests that the Ub-PCNA/Pol η interaction requires the formation of a structured binding interface, which is dictated by the inherent flexibility of Ub-PCNA. | |||||||||
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_6339.map.gz | 3.7 MB | EMDB map data format | |
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Header (meta data) | emd-6339-v30.xml emd-6339.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | 400_6339.gif 80_6339.gif | 43.4 KB 4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6339 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6339 | HTTPS FTP |
-Validation report
Summary document | emd_6339_validation.pdf.gz | 292.9 KB | Display | EMDB validaton report |
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Full document | emd_6339_full_validation.pdf.gz | 292.5 KB | Display | |
Data in XML | emd_6339_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6339 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6339 | HTTPS FTP |
-Related structure data
Related structure data | 3ja9MC 3jaaMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6339.map.gz / Format: CCP4 / Size: 4.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Ub-PCNA/Pol eta/DNA ternary complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.14 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 : Ub-PCNA/Pol eta/DNA
Entire | Name: Ub-PCNA/Pol eta/DNA |
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Components |
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-Supramolecule #1000: Ub-PCNA/Pol eta/DNA
Supramolecule | Name: Ub-PCNA/Pol eta/DNA / type: sample / ID: 1000 / Details: The sample was monodisperse Oligomeric state: Monomeric catalytic core of Pol eta binds to one homotrimeric Ub-PCNA Number unique components: 2 |
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Molecular weight | Experimental: 200 KDa / Theoretical: 200 KDa / Method: Chemical crosslinking, SDS-PAGE |
-Macromolecule #1: Monoubiquitinated PCNA
Macromolecule | Name: Monoubiquitinated PCNA / type: protein_or_peptide / ID: 1 / Oligomeric state: trimer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Experimental: 120 KDa / Theoretical: 120 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) |
-Macromolecule #2: Pol eta
Macromolecule | Name: Pol eta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: RW644 / Recombinant plasmid: pJM879 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 8 / Details: 50mM Tris-HCl, 5mM MgCl2 |
Staining | Type: NEGATIVE Details: Grids with adsorbed protein floated on two 20ul drops of 2% w/v uranyl acetate solution for 30 seconds |
Grid | Details: Continuous carbon coated copper grids (Ted Pella), glow-discharged for 30 seconds |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | JEOL 2010 |
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Date | Nov 12, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 18 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Image processing
CTF correction | Details: Particles |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 7330 |
Final two d classification | Number classes: 227 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-3ja9: PDB-3jaa: |