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- PDB-8a8w: Mycobacterium tuberculosis ClpC1 hexamer structure bound to the n... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8a8w | ||||||||||||
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Title | Mycobacterium tuberculosis ClpC1 hexamer structure bound to the natural product antibiotic Ecumycin (class 1) | ||||||||||||
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![]() | CHAPERONE / hexamer / tuberculosis / drug target / protein quality control | ||||||||||||
Function / homology | ![]() protein folding chaperone / peptidoglycan-based cell wall / cellular response to heat / protein homodimerization activity / ATP hydrolysis activity / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.29 Å | ||||||||||||
![]() | Felix, J. / Fraga, H. / Gragera, M. / Bueno, T. / Weinhaeupl, K. | ||||||||||||
Funding support | European Union, 3items
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![]() | ![]() Title: Structure of the drug target ClpC1 unfoldase in action provides insights on antibiotic mechanism of action. Authors: Katharina Weinhäupl / Marcos Gragera / M Teresa Bueno-Carrasco / Rocío Arranz / Olga Krandor / Tatos Akopian / Raquel Soares / Eric Rubin / Jan Felix / Hugo Fraga / ![]() ![]() ![]() ![]() Abstract: The unfoldase ClpC1 is one of the most exciting drug targets against tuberculosis. This AAA+ unfoldase works in cooperation with the ClpP1P2 protease and is the target of at least four natural ...The unfoldase ClpC1 is one of the most exciting drug targets against tuberculosis. This AAA+ unfoldase works in cooperation with the ClpP1P2 protease and is the target of at least four natural product antibiotics: cyclomarin, ecumicin, lassomycin, and rufomycin. Although these molecules are promising starting points for drug development, their mechanisms of action remain largely unknown. Taking advantage of a middle domain mutant, we determined the first structure of Mycobacterium tuberculosis ClpC1 in its apo, cyclomarin-, and ecumicin-bound states via cryo-EM. The obtained structure displays features observed in other members of the AAA+ family and provides a map for further drug development. While the apo and cyclomarin-bound structures are indistinguishable and have N-terminal domains that are invisible in their respective EM maps, around half of the ecumicin-bound ClpC1 particles display three of their six N-terminal domains in an extended conformation. Our structural observations suggest a mechanism where ecumicin functions by mimicking substrate binding, leading to ATPase activation and changes in protein degradation profile. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 607.4 KB | Display | ![]() |
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PDB format | ![]() | 493.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 102 KB | Display | |
Data in CIF | ![]() | 152 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 15242MC ![]() 8a8uC ![]() 8a8vC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 94758.695 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P9WPC9, Hydrolases; Acting on peptide bonds (peptidases) #2: Protein/peptide | | Mass: 2145.636 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The exact sequence of the polypeptide is unknown. / Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-ADP / Has ligand of interest | N | |
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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: Mycobacterium tuberculosis ClpC1 bound to the natural product antibiotic Ecumicin Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.567 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 Details: Hepes pH 7.4 50 mM, NaCl 100 mM, 10 mM MgCl2, ATP 1mM |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 10 microM ClpC1 with 30 microM Ecumicin |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: OTHER / Nominal defocus max: 3100 nm / Nominal defocus min: 1200 nm |
Image recording | Average exposure time: 40 sec. / Electron dose: 32.2 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45698 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Details: Initial model source is a trimmed AlphaFold model of Mycobacterium tuberculosis ClpC1 (https://alphafold.ebi.ac.uk/entry/P9WPC8). | ||||||||||||||||||||||||||||||||
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