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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21115 | |||||||||
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Title | Structure of DNA Polymerase Zeta/DNA/dNTP Ternary Complex | |||||||||
![]() | cryosparc map | |||||||||
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![]() | DNA REPLICATION / DNA REPAIR / TRANSLESION DNA SYNTHESIS / DNA POLYMERASE / DNA BINDING PROTEIN | |||||||||
Function / homology | ![]() 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 / error-prone translesion synthesis / mismatch repair / 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 | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Malik R / Kopylov M / Jain R / Ubarrextena-Belandia I / Aggarwal AK | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and mechanism of B-family DNA polymerase ζ specialized for translesion DNA synthesis. Authors: Radhika Malik / Mykhailo Kopylov / Yacob Gomez-Llorente / Rinku Jain / Robert E Johnson / Louise Prakash / Satya Prakash / Iban Ubarretxena-Belandia / Aneel K Aggarwal / ![]() ![]() Abstract: DNA polymerase ζ (Polζ) belongs to the same B-family as high-fidelity replicative polymerases, yet is specialized for the extension reaction in translesion DNA synthesis (TLS). Despite its ...DNA polymerase ζ (Polζ) belongs to the same B-family as high-fidelity replicative polymerases, yet is specialized for the extension reaction in translesion DNA synthesis (TLS). Despite its importance in TLS, the structure of Polζ is unknown. We present cryo-EM structures of the Saccharomyces cerevisiae Polζ holoenzyme in the act of DNA synthesis (3.1 Å) and without DNA (4.1 Å). Polζ displays a pentameric ring-like architecture, with catalytic Rev3, accessory Pol31' Pol32 and two Rev7 subunits forming an uninterrupted daisy chain of protein-protein interactions. We also uncover the features that impose high fidelity during the nucleotide-incorporation step and those that accommodate mismatches and lesions during the extension reaction. Collectively, we decrypt the molecular underpinnings of Polζ's role in TLS and provide a framework for new cancer therapeutics. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 58.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.7 KB 17.7 KB | Display Display | ![]() |
Images | ![]() | 69 KB | ||
Filedesc metadata | ![]() | 7.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 539.5 KB | Display | ![]() |
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Full document | ![]() | 539.1 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 7.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6v93MC ![]() 6v8pC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | cryosparc map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07325 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : structure of DNA complex
+Supramolecule #1: structure of DNA complex
+Macromolecule #1: DNA polymerase zeta catalytic subunit
+Macromolecule #2: DNA polymerase zeta processivity subunit
+Macromolecule #3: DNA polymerase delta small subunit
+Macromolecule #4: DNA polymerase delta subunit 3
+Macromolecule #5: DNA
+Macromolecule #6: IRON/SULFUR CLUSTER
+Macromolecule #7: CALCIUM ION
+Macromolecule #8: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
+Macromolecule #9: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.8 |
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Sugar embedding | Material: vitreous ice |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 71.63 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 156067 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |