+Open data
-Basic information
Entry | Database: PDB / ID: 6po3 | |||||||||
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Title | ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 3 | |||||||||
Components |
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Keywords | CHAPERONE / Protein degradation / AAA+ protease complex | |||||||||
Function / homology | Function and homology information protein denaturation / HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / positive regulation of programmed cell death / response to temperature stimulus / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / proteasomal protein catabolic process ...protein denaturation / HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / positive regulation of programmed cell death / response to temperature stimulus / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / proteasomal protein catabolic process / serine-type peptidase activity / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / response to radiation / disordered domain specific binding / unfolded protein binding / protein folding / peptidase activity / ATPase binding / response to heat / protease binding / protein dimerization activity / cell division / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.28 Å | |||||||||
Authors | Fei, X. / Jenni, S. / Harrison, S.C. / Sauer, R.T. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Elife / Year: 2020 Title: Structures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate. Authors: Xue Fei / Tristan A Bell / Simon Jenni / Benjamin M Stinson / Tania A Baker / Stephen C Harrison / Robert T Sauer / Abstract: ClpXP is an ATP-dependent protease in which the ClpX AAA+ motor binds, unfolds, and translocates specific protein substrates into the degradation chamber of ClpP. We present cryo-EM studies of the ...ClpXP is an ATP-dependent protease in which the ClpX AAA+ motor binds, unfolds, and translocates specific protein substrates into the degradation chamber of ClpP. We present cryo-EM studies of the enzyme that show how asymmetric hexameric rings of ClpX bind symmetric heptameric rings of ClpP and interact with protein substrates. Subunits in the ClpX hexamer assume a spiral conformation and interact with two-residue segments of substrate in the axial channel, as observed for other AAA+ proteases and protein-remodeling machines. Strictly sequential models of ATP hydrolysis and a power stroke that moves two residues of the substrate per translocation step have been inferred from these structural features for other AAA+ unfoldases, but biochemical and single-molecule biophysical studies indicate that ClpXP operates by a probabilistic mechanism in which five to eight residues are translocated for each ATP hydrolyzed. We propose structure-based models that could account for the functional results. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6po3.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6po3.ent.gz | 919 KB | Display | PDB format |
PDBx/mmJSON format | 6po3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6po3_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6po3_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6po3_validation.xml.gz | 87.5 KB | Display | |
Data in CIF | 6po3_validation.cif.gz | 131.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/6po3 ftp://data.pdbj.org/pub/pdb/validation_reports/po/6po3 | HTTPS FTP |
-Related structure data
Related structure data | 20408MC 6po1C 6podC 6posC 6pp5C 6pp6C 6pp7C 6pp8C 6ppeC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 39835.129 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clpX, BUE81_06555 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: A0A1Q9L861, UniProt: P0A6H1*PLUS #2: Protein | Mass: 23212.650 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clpP, A1WS_00920 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 References: UniProt: S1IIE7, UniProt: P0A6G7*PLUS, endopeptidase Clp #3: Protein/peptide | | Mass: 666.791 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 #4: Chemical | ChemComp-AGS / #5: 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 |
-Sample preparation
Component | Name: ClpX-ClpP-substrate-ATPrS / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) / Strain: ER2566 |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: ER2566 |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus min: -800 nm / Calibrated defocus max: -2500 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 60 sec. / Electron dose: 56 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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Image processing | Details: 2X binned and motioncor2 corrected | ||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26592 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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Refine LS restraints |
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