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Open data
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Basic information
Entry | Database: PDB / ID: 7s0t | ||||||
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Title | Structure of DNA polymerase zeta with mismatched DNA | ||||||
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![]() | DNA BINDING PROTEIN/DNA / ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() delta DNA polymerase complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Malik, R. / Ubarretxena, I.B. / Aggarwal, A.K. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 423.7 KB | Display | ![]() |
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PDB format | ![]() | 317.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 24793MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-DNA polymerase zeta ... , 2 types, 3 molecules ADE
#1: Protein | Mass: 177068.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: REV3, PSO1, YPL167C, P2535 / Production host: ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 28791.654 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: REV7, YIL139C / Production host: ![]() ![]() ![]() |
-DNA polymerase delta ... , 2 types, 2 molecules FG
#3: Protein | ![]() Mass: 55987.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: PACBIOSEQ_LOCUS3277, PACBIOSEQ_LOCUS3308 / Production host: ![]() ![]() ![]() |
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#4: Protein | ![]() Mass: 40377.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: POL32, YJR043C, J1626 / Production host: ![]() ![]() ![]() |
-DNA chain , 1 types, 2 molecules PT
#5: DNA chain | Mass: 9232.955 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 34 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/DCP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/DCP.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-SF4 / ![]() |
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#7: Chemical | ChemComp-CA / |
#8: Chemical | ChemComp-DCP / ![]() |
#9: Water | ChemComp-HOH / ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Structure of DNA complex / Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: ![]() ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7.8 |
Specimen | Embedding applied: YES / Shadowing applied: NO / Staining applied![]() ![]() |
EM embedding | Material: Vitreous ice |
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![]() |
Image recording | Electron dose: 64.82 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120985 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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