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Open data
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Basic information
Entry | Database: PDB / ID: 7pu7 | ||||||
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Title | DNA polymerase from M. tuberculosis | ||||||
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![]() | REPLICATION / Inhibitor / DNA Polymerase | ||||||
Function / homology | ![]() 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
![]() | Borsellini, A. / Lamers, M.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: DNA-Dependent Binding of Nargenicin to DnaE1 Inhibits Replication in . Authors: Melissa D Chengalroyen / Mandy K Mason / Alessandro Borsellini / Raffaella Tassoni / Garth L Abrahams / Sasha Lynch / Yong-Mo Ahn / Jon Ambler / Katherine Young / Brendan M Crowley / David B ...Authors: Melissa D Chengalroyen / Mandy K Mason / Alessandro Borsellini / Raffaella Tassoni / Garth L Abrahams / Sasha Lynch / Yong-Mo Ahn / Jon Ambler / Katherine Young / Brendan M Crowley / David B Olsen / Digby F Warner / Clifton E Barry Iii / Helena I M Boshoff / Meindert H Lamers / Valerie Mizrahi / ![]() ![]() ![]() Abstract: Natural products provide a rich source of potential antimicrobials for treating infectious diseases for which drug resistance has emerged. Foremost among these diseases is tuberculosis. Assessment of ...Natural products provide a rich source of potential antimicrobials for treating infectious diseases for which drug resistance has emerged. Foremost among these diseases is tuberculosis. Assessment of the antimycobacterial activity of nargenicin, a natural product that targets the replicative DNA polymerase of , revealed that it is a bactericidal genotoxin that induces a DNA damage response in () and inhibits growth by blocking the replicative DNA polymerase, DnaE1. Cryo-electron microscopy revealed that binding of nargenicin to DnaE1 requires the DNA substrate such that nargenicin is wedged between the terminal base pair and the polymerase and occupies the position of both the incoming nucleotide and templating base. Comparative analysis across three bacterial species suggests that the activity of nargenicin is partly attributable to the DNA binding affinity of the replicative polymerase. This work has laid the foundation for target-led drug discovery efforts focused on DnaE1. | ||||||
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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 | ![]() | 239.4 KB | Display | ![]() |
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PDB format | ![]() | 183.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 850.9 KB | Display | ![]() |
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Full document | ![]() | 858.9 KB | Display | |
Data in XML | ![]() | 38.7 KB | Display | |
Data in CIF | ![]() | 58.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 13654MC 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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1 |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 129479.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: dnaE1, dnaE, C0094_08490, DSI38_14925, E5M05_02710, E5M52_02685, E5M78_02685, ERS007703_00014, ERS007722_00056, ERS013471_00953, ERS094182_01482, F6W99_00105, SAMEA2683035_03173 Production host: ![]() References: UniProt: A0A045J099, DNA-directed DNA polymerase |
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-DNA/RNA hybrid , 2 types, 2 molecules TP
#2: DNA/RNA hybrid | Mass: 5944.902 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA/RNA hybrid | Mass: 4197.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 7 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/82W.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/82W.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-82W / [( | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: DNA polymerase from M. tuberculosis / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 129.3 kDa/nm / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() | |||||||||||||||||||||||||
Buffer solution | pH: 7 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid type: Quantifoil R2/1 | |||||||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 76 % / Chamber temperature: 277 K |
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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 / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 196709 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |