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Yorodumi- EMDB-2409: The architecture of yeast DNA polymerase 'zeta'. Electron microsc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2409 | |||||||||
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Title | The architecture of yeast DNA polymerase 'zeta'. Electron microscopy reconstruction of the heterotetrameric complex Rev3-Rev7-Pol31-Pol32. | |||||||||
Map data | Map of Pol-zeta-d heterotetramer by negative stain | |||||||||
Sample |
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Keywords | Translesion DNA synthesis / DNA repair / DNA replication / DNA polymerase zeta / genome integrity / cancer | |||||||||
Function / homology | Function and homology information delta DNA polymerase complex / DNA amplification / zeta DNA polymerase complex / RNA-templated DNA biosynthetic process / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / DNA replication, removal of RNA primer / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI ...delta DNA polymerase complex / DNA amplification / zeta DNA polymerase complex / RNA-templated DNA biosynthetic process / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / DNA replication, removal of RNA primer / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / lagging strand elongation / double-strand break repair via break-induced replication / postreplication repair / DNA metabolic process / DNA strand elongation involved in DNA replication / error-free translesion synthesis / leading strand elongation / mismatch repair / error-prone translesion synthesis / nucleotide-excision repair / double-strand break repair via homologous recombination / base-excision repair / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / chromatin / mitochondrion / DNA binding / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 23.0 Å | |||||||||
Authors | Gomez-Llorente Y / Malik R / Jain R / Roy Choudhury J / Johnson RE / Prakash L / Prakash S / Ubarretxena-Belandia I / Aggarwal AK | |||||||||
Citation | Journal: Cell Rep / Year: 2013 Title: The architecture of yeast DNA polymerase ζ. Authors: Yacob Gómez-Llorente / Radhika Malik / Rinku Jain / Jayati Roy Choudhury / Robert E Johnson / Louise Prakash / Satya Prakash / Iban Ubarretxena-Belandia / Aneel K Aggarwal / Abstract: DNA polymerase ζ (Polζ) is specialized for the extension step of translesion DNA synthesis (TLS). Despite its central role in maintaining genome integrity, little is known about its overall ...DNA polymerase ζ (Polζ) is specialized for the extension step of translesion DNA synthesis (TLS). Despite its central role in maintaining genome integrity, little is known about its overall architecture. Initially identified as a heterodimer of the catalytic subunit Rev3 and the accessory subunit Rev7, yeast Polζ has recently been shown to form a stable four-subunit enzyme (Polζ-d) upon the incorporation of Pol31 and Pol32, the accessory subunits of yeast Polδ. To understand the 3D architecture and assembly of Polζ and Polζ-d, we employed electron microscopy. We show here how the catalytic and accessory subunits of Polζ and Polζ-d are organized relative to each other. In particular, we show that Polζ-d has a bilobal architecture resembling the replicative polymerases and that Pol32 lies in proximity to Rev7. Collectively, our study provides views of Polζ and Polζ-d and a structural framework for understanding their roles in DNA damage bypass. | |||||||||
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_2409.map.gz | 1.8 MB | EMDB map data format | |
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Header (meta data) | emd-2409-v30.xml emd-2409.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
Images | emd_2409.jpg | 20.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2409 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2409 | HTTPS FTP |
-Validation report
Summary document | emd_2409_validation.pdf.gz | 222.3 KB | Display | EMDB validaton report |
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Full document | emd_2409_full_validation.pdf.gz | 221.4 KB | Display | |
Data in XML | emd_2409_validation.xml.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2409 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2409 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2409.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map of Pol-zeta-d heterotetramer by negative stain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.78 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 : Polymerase Zeta heterotetramer of Saccharomyces cerevisiae
Entire | Name: Polymerase Zeta heterotetramer of Saccharomyces cerevisiae |
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Components |
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-Supramolecule #1000: Polymerase Zeta heterotetramer of Saccharomyces cerevisiae
Supramolecule | Name: Polymerase Zeta heterotetramer of Saccharomyces cerevisiae type: sample / ID: 1000 / Details: Rev3:Rev7:Pol31:Pol32N 1:1:1:1 / Oligomeric state: Heterotetramer / Number unique components: 4 |
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Molecular weight | Experimental: 300 KDa / Theoretical: 298 KDa |
-Macromolecule #1: DNA Polymerase 'Zeta' processivity subunit
Macromolecule | Name: DNA Polymerase 'Zeta' processivity subunit / type: protein_or_peptide / ID: 1 / Name.synonym: Rev7 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: Cytoplasm |
Molecular weight | Experimental: 28 KDa / Theoretical: 28 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: PETDuet |
Sequence | UniProtKB: DNA polymerase zeta processivity subunit GO: error-free translesion synthesis, error-prone translesion synthesis InterPro: HORMA domain |
-Macromolecule #2: DNA Polymerase 'Delta' small subunit
Macromolecule | Name: DNA Polymerase 'Delta' small subunit / type: protein_or_peptide / ID: 2 / Name.synonym: Pol31 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: Cytoplasm |
Molecular weight | Experimental: 55 KDa / Theoretical: 55 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: PETDuet |
Sequence | UniProtKB: DNA polymerase delta small subunit GO: DNA replication, removal of RNA primer, mismatch repair, base-excision repair InterPro: DNA polymerase alpha/delta/epsilon, subunit B, DNA polymerase delta/II small subunit family |
-Macromolecule #3: DNA Polymerase 'Delta' subunit 3
Macromolecule | Name: DNA Polymerase 'Delta' subunit 3 / type: protein_or_peptide / ID: 3 / Name.synonym: Pol32 Details: We are using the N-terminal part of this protein. For further details, check the associated publication. Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: Cytoplasm |
Molecular weight | Experimental: 40 KDa / Theoretical: 40 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: PETDuet |
Sequence | UniProtKB: DNA polymerase delta subunit 3 GO: DNA replication, removal of RNA primer, mismatch repair, base-excision repair |
-Macromolecule #4: DNA Polymerase 'Zeta' catalytic subunit
Macromolecule | Name: DNA Polymerase 'Zeta' catalytic subunit / type: protein_or_peptide / ID: 4 / Name.synonym: Rev3 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: Cytoplasm |
Molecular weight | Experimental: 173 KDa / Theoretical: 173 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: PETDuet |
Sequence | UniProtKB: DNA polymerase zeta catalytic subunit GO: error-free translesion synthesis, error-prone translesion synthesis, DNA replication InterPro: DNA-directed DNA polymerase, family B, DNA-directed DNA polymerase, family B, conserved site, DNA-directed DNA polymerase, family B, exonuclease domain, DNA-directed DNA polymerase, family ...InterPro: DNA-directed DNA polymerase, family B, DNA-directed DNA polymerase, family B, conserved site, DNA-directed DNA polymerase, family B, exonuclease domain, DNA-directed DNA polymerase, family B, multifunctional domain, DNA polymerase, palm domain superfamily, Ribonuclease H-like superfamily, C4-type zinc-finger of DNA polymerase delta |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 / Details: 25mM Tris pH 8.0, 250mM NaCl |
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Staining | Type: NEGATIVE Details: 2 ul aliquots were adsorbed onto glow-discharged carbon coated copper grids, and negatively stained with 2% uranyl acetate. |
Grid | Details: Glow discharged carbon coated copper grids. |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | JEOL 2100F |
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Temperature | Min: 80 K / Max: 298 K / Average: 293 K |
Date | Jan 1, 2011 |
Image recording | Category: CCD / Film or detector model: GENERIC TVIPS / Average electron dose: 10 e/Å2 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 63450 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 40000 |
Sample stage | Specimen holder model: JEOL |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Xmipp, EMAN2, Spider / Number images used: 14844 |