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Yorodumi- PDB-8xop: Cryo-EM structure of ClpP1P2 in complex with ADEP1 from Streptomy... -
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-Basic information
Entry | Database: PDB / ID: 8xop | ||||||
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Title | Cryo-EM structure of ClpP1P2 in complex with ADEP1 from Streptomyces hawaiiensis | ||||||
Components |
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Keywords | HYDROLASE / protease / protein degradation / proteostasis / proteolysis | ||||||
Function / homology | Function and homology information endopeptidase Clp / ATP-dependent peptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | Streptomyces hawaiiensis (bacteria) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Xu, X. / Long, F. | ||||||
Funding support | China, 1items
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Citation | Journal: mBio / Year: 2024 Title: Structural insights into the Clp protein degradation machinery. Authors: Xiaolong Xu / Yanhui Wang / Wei Huang / Danyang Li / Zixin Deng / Feng Long / Abstract: The Clp protease system is important for maintaining proteostasis in bacteria. It consists of ClpP serine proteases and an AAA+ Clp-ATPase such as ClpC1. The hexameric ATPase ClpC1 utilizes the ...The Clp protease system is important for maintaining proteostasis in bacteria. It consists of ClpP serine proteases and an AAA+ Clp-ATPase such as ClpC1. The hexameric ATPase ClpC1 utilizes the energy of ATP binding and hydrolysis to engage, unfold, and translocate substrates into the proteolytic chamber of homo- or hetero-tetradecameric ClpP for degradation. The assembly between the hetero-tetradecameric ClpP1P2 chamber and the Clp-ATPases containing tandem ATPase domains from the same species has not been studied in depth. Here, we present cryo-EM structures of the substrate-bound ClpC1:shClpP1P2 from , and shClpP1P2 in complex with ADEP1, a natural compound produced by and known to cause over-activation and dysregulation of the ClpP proteolytic core chamber. Our structures provide detailed information on the shClpP1-shClpP2, shClpP2-ClpC1, and ADEP1-shClpP1/P2 interactions, reveal conformational transition of ClpC1 during the substrate translocation, and capture a rotational ATP hydrolysis mechanism likely dominated by the D1 ATPase activity of chaperones.IMPORTANCEThe Clp-dependent proteolysis plays an important role in bacterial homeostasis and pathogenesis. The ClpP protease system is an effective drug target for antibacterial therapy. can produce a class of potent acyldepsipeptide antibiotics such as ADEP1, which could affect the ClpP protease activity. Although hosts one of the most intricate ClpP systems in nature, very little was known about its Clp protease mechanism and the impact of ADEP molecules on ClpP. The significance of our research is in dissecting the functional mechanism of the assembled Clp degradation machinery, as well as the interaction between ADEP1 and the ClpP proteolytic chamber, by solving high-resolution structures of the substrate-bound Clp system in . The findings shed light on our understanding of the Clp-dependent proteolysis in bacteria, which will enhance the development of antimicrobial drugs targeting the Clp protease system, and help fighting against bacterial multidrug resistance. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xop.cif.gz | 448.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xop.ent.gz | 360.6 KB | Display | PDB format |
PDBx/mmJSON format | 8xop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/8xop ftp://data.pdbj.org/pub/pdb/validation_reports/xo/8xop | HTTPS FTP |
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-Related structure data
Related structure data | 38537MC 8xn4C 8xonC 8xooC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 22632.605 Da / Num. of mol.: 7 / Mutation: S113A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces hawaiiensis (bacteria) / Gene: clpP1, clpP, CEB94_14110 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5B9BGY8, endopeptidase Clp #2: Protein | Mass: 24058.240 Da / Num. of mol.: 7 / Mutation: S131A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces hawaiiensis (bacteria) / Gene: clpP2, clpP, CEB94_14105 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5B9BIX9, endopeptidase Clp #3: Protein/peptide | 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 |
-Sample preparation
Component | Name: ClpP1,ClpP2 / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Streptomyces hawaiiensis (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.19.2_4158: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C7 (7 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 504306 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 147.2 Å2 | ||||||||||||||||||||||||
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