+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24793 | |||||||||
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Title | Structure of DNA polymerase zeta with mismatched DNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DNA repair / DNA replication / translesion DNA synthesis / DNA polymerase / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information delta DNA polymerase complex / DNA amplification / zeta DNA polymerase complex / RNA-templated DNA biosynthetic process / 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 ...delta DNA polymerase complex / DNA amplification / zeta DNA polymerase complex / RNA-templated DNA biosynthetic process / 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 / DNA metabolic process / DNA strand elongation involved in DNA replication / error-free translesion synthesis / leading strand elongation / 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 Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||
Authors | Malik R / Ubarretxena IB | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Cryo-EM structure of translesion DNA synthesis polymerase ζ with a base pair mismatch. Authors: Radhika Malik / Robert E Johnson / Louise Prakash / Satya Prakash / Iban Ubarretxena-Belandia / Aneel K Aggarwal / Abstract: The B-family multi-subunit DNA polymerase ζ (Polζ) is important for translesion DNA synthesis (TLS) during replication, due to its ability to extend synthesis past nucleotides opposite DNA lesions ...The B-family multi-subunit DNA polymerase ζ (Polζ) is important for translesion DNA synthesis (TLS) during replication, due to its ability to extend synthesis past nucleotides opposite DNA lesions and mismatched base pairs. We present a cryo-EM structure of Saccharomyces cerevisiae Polζ with an A:C mismatch at the primer terminus. The structure shows how the Polζ active site responds to the mismatched duplex DNA distortion, including the loosening of key protein-DNA interactions and a fingers domain in an "open" conformation, while the incoming dCTP is still able to bind for the extension reaction. The structure of the mismatched DNA-Polζ ternary complex reveals insights into mechanisms that either stall or favor continued DNA synthesis in eukaryotes. | |||||||||
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_24793.map.gz | 31.5 MB | EMDB map data format | |
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Header (meta data) | emd-24793-v30.xml emd-24793.xml | 17.2 KB 17.2 KB | Display Display | EMDB header |
Images | emd_24793.png | 121.5 KB | ||
Filedesc metadata | emd-24793.cif.gz | 7.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24793 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24793 | HTTPS FTP |
-Validation report
Summary document | emd_24793_validation.pdf.gz | 496.7 KB | Display | EMDB validaton report |
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Full document | emd_24793_full_validation.pdf.gz | 496.3 KB | Display | |
Data in XML | emd_24793_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_24793_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24793 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24793 | HTTPS FTP |
-Related structure data
Related structure data | 7s0tMC 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_24793.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.096 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 : 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 (30-MER)
+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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Sugar embedding | Material: Vitreous ice |
Vitrification | Cryogen name: ETHANE |
-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: 64.82 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 120985 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |