+Open data
-Basic information
Entry | Database: PDB / ID: 6vfs | ||||||||||||
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Title | ClpXP from Neisseria meningitidis - Conformation A | ||||||||||||
Components |
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Keywords | HYDROLASE / Complex / AAA+ / protease / ClpP / ClpX | ||||||||||||
Function / homology | Function and homology information HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / unfolded protein binding / peptidase activity / ATPase binding ...HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / unfolded protein binding / peptidase activity / ATPase binding / protein dimerization activity / cell division / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Neisseria meningitidis (bacteria) Escherichia coli BL21 (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
Authors | Ripstein, Z.A. / Vahidi, S. / Houry, W.A. / Rubinstein, J.L. / Kay, L.E. | ||||||||||||
Funding support | Canada, 3items
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Citation | Journal: Elife / Year: 2020 Title: A processive rotary mechanism couples substrate unfolding and proteolysis in the ClpXP degradation machinery. Authors: Zev A Ripstein / Siavash Vahidi / Walid A Houry / John L Rubinstein / Lewis E Kay / Abstract: The ClpXP degradation machine consists of a hexameric AAA+ unfoldase (ClpX) and a pair of heptameric serine protease rings (ClpP) that unfold, translocate, and subsequently degrade client proteins. ...The ClpXP degradation machine consists of a hexameric AAA+ unfoldase (ClpX) and a pair of heptameric serine protease rings (ClpP) that unfold, translocate, and subsequently degrade client proteins. ClpXP is an important target for drug development against infectious diseases. Although structures are available for isolated ClpX and ClpP rings, it remains unknown how symmetry mismatched ClpX and ClpP work in tandem for processive substrate translocation into the ClpP proteolytic chamber. Here, we present cryo-EM structures of the substrate-bound ClpXP complex from at 2.3 to 3.3 Å resolution. The structures allow development of a model in which the sequential hydrolysis of ATP is coupled to motions of ClpX loops that lead to directional substrate translocation and ClpX rotation relative to ClpP. Our data add to the growing body of evidence that AAA+ molecular machines generate translocating forces by a common mechanism. | ||||||||||||
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 | 6vfs.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6vfs.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 6vfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vfs_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6vfs_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6vfs_validation.xml.gz | 107.9 KB | Display | |
Data in CIF | 6vfs_validation.cif.gz | 156.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/6vfs ftp://data.pdbj.org/pub/pdb/validation_reports/vf/6vfs | HTTPS FTP |
-Related structure data
Related structure data | 21187MC 6vfxC 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
-ATP-dependent Clp protease ... , 2 types, 20 molecules EAFCBDLOPQRSTUHIJKMN
#1: Protein | Mass: 45139.438 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) Gene: clpX, COH52_00090, COI09_01415, ERS514410_00003, NCTC8554_00172 Plasmid: pet28a / Details (production host): 6His tag with TEV site / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0Y4ZJG4, UniProt: Q9JYY3*PLUS #3: Protein | Mass: 22729.967 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: clpP, COI09_01760, ERS514410_00057 / Plasmid: pet28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A0Y5K536, UniProt: Q9JZ38*PLUS, endopeptidase Clp |
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-Protein/peptide , 1 types, 1 molecules G
#2: Protein/peptide | Mass: 613.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) |
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-Non-polymers , 3 types, 10 molecules
#4: Chemical | ChemComp-ATP / #5: Chemical | ChemComp-MG / #6: Chemical | |
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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 |
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Molecular weight | Value: 0.86 MDa / Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: Bl21(DE3) / Plasmid: pet28a | ||||||||||||||||||||||||||||
Buffer solution | pH: 8.5 Details: Buffer pH was measured as 8.2 at room temperature corresponding to a pH of 8.5 at 4 degrees, the temperature at which the complex was held before vitrification | ||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Mono-disperse complexes | ||||||||||||||||||||||||||||
Specimen support | Details: Home-made gold grids were inspected before use / Grid material: COPPER/RHODIUM / Grid mesh size: 400 divisions/in. / Grid type: Homemade | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blotted for 15 seconds at an offset of -5 mm |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 1700 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 70 K |
Image recording | Average exposure time: 60 sec. / Electron dose: 43 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2680 |
Image scans | Width: 4096 / Height: 4096 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 466549 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110696 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3HWS Accession code: 3HWS / Source name: PDB / Type: experimental model |