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Yorodumi- PDB-6wr2: ClpP and ClpX IGF loop in ClpX-ClpP complex bound to ssrA tagged GFP -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wr2 | ||||||
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Title | ClpP and ClpX IGF loop in ClpX-ClpP complex bound to ssrA tagged GFP | ||||||
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 / 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 Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å | ||||||
Authors | Fei, X. / Sauer, R.T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2020 Title: Structural basis of ClpXP recognition and unfolding of ssrA-tagged substrates. Authors: Xue Fei / Tristan A Bell / Sarah R Barkow / Tania A Baker / Robert T Sauer / Abstract: When ribosomes fail to complete normal translation, all cells have mechanisms to ensure degradation of the resulting partial proteins to safeguard proteome integrity. In and other eubacteria, the ...When ribosomes fail to complete normal translation, all cells have mechanisms to ensure degradation of the resulting partial proteins to safeguard proteome integrity. In and other eubacteria, the tmRNA system rescues stalled ribosomes and adds an ssrA tag or degron to the C-terminus of the incomplete protein, which directs degradation by the AAA+ ClpXP protease. Here, we present cryo-EM structures of ClpXP bound to the ssrA degron. C-terminal residues of the ssrA degron initially bind in the top of an otherwise closed ClpX axial channel and subsequently move deeper into an open channel. For short-degron protein substrates, we show that unfolding can occur directly from the initial closed-channel complex. For longer degron substrates, our studies illuminate how ClpXP transitions from specific recognition into a nonspecific unfolding and translocation machine. Many AAA+ proteases and protein-remodeling motors are likely to employ similar multistep recognition and engagement strategies. | ||||||
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 | 6wr2.cif.gz | 895.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wr2.ent.gz | 739.1 KB | Display | PDB format |
PDBx/mmJSON format | 6wr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wr2_validation.pdf.gz | 879.3 KB | Display | wwPDB validaton report |
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Full document | 6wr2_full_validation.pdf.gz | 879.4 KB | Display | |
Data in XML | 6wr2_validation.xml.gz | 71 KB | Display | |
Data in CIF | 6wr2_validation.cif.gz | 111.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/6wr2 ftp://data.pdbj.org/pub/pdb/validation_reports/wr/6wr2 | HTTPS FTP |
-Related structure data
Related structure data | 21875MC 6wrfC 6wsgC 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: 42355.812 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: clpX, lopC, b0438, JW0428 / Plasmid: pacyc / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P0A6H1 #2: Protein | Mass: 23468.869 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: clpP, lopP, b0437, JW0427 / Plasmid: HTUA / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P0A6G7, endopeptidase Clp #3: Water | ChemComp-HOH / | |
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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-GFPssrA-ATP/ATPrS / Type: COMPLEX / Entity ID: #1-#2 / 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 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: rapid mixing of ClpX, ClpP, ATPrS with GFPssrA substrate and ATP. | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / 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 TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 45000 X / Nominal defocus max: -2500 nm / Nominal defocus min: -800 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: 54 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4525 |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 334069 / Details: with multibody refinement / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6PPE Accession code: 6PPE / Source name: PDB / Type: experimental model |