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Yorodumi- PDB-8xoo: Cryo-EM structure of the ClpC1:ClpP1P2 degradation complex in Str... -
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-Basic information
Entry | Database: PDB / ID: 8xoo | ||||||
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Title | Cryo-EM structure of the ClpC1:ClpP1P2 degradation complex in Streptomyces hawaiiensis | ||||||
Components |
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Keywords | HYDROLASE / protease / protein degradation / proteostasis / proteolysis | ||||||
Function / homology | Function and homology information endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / cellular response to heat / serine-type endopeptidase activity / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptomyces hawaiiensis (bacteria) Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.84 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 | 8xoo.cif.gz | 1020.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xoo.ent.gz | 849.1 KB | Display | PDB format |
PDBx/mmJSON format | 8xoo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xoo_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 8xoo_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8xoo_validation.xml.gz | 163.3 KB | Display | |
Data in CIF | 8xoo_validation.cif.gz | 246.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/8xoo ftp://data.pdbj.org/pub/pdb/validation_reports/xo/8xoo | HTTPS FTP |
-Related structure data
Related structure data | 38536MC 8xn4C 8xonC 8xopC 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
-ATP-dependent Clp protease proteolytic ... , 2 types, 14 molecules ABCDEFGHIJKLMN
#1: Protein | Mass: 24216.336 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: 22807.850 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 |
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-Protein / Protein/peptide , 2 types, 7 molecules RQPOTSX
#3: Protein | Mass: 77312.055 Da / Num. of mol.: 6 / Mutation: E284A,F440A,E622A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces hawaiiensis (bacteria) / Gene: CEB94_23085 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6G5RIJ6 #4: Protein/peptide | | Mass: 2060.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Plasmid details: milk |
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-Non-polymers , 3 types, 19 molecules
#5: Chemical | ChemComp-ATP / #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-ADP / |
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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 |
-Sample preparation
Component | Name: ClpP1,ClpP2,ClpC1,casein / Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES |
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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 |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / 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 FIELD / Nominal defocus max: 2500 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: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 1.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 183537 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||
Refine LS restraints |
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