+Open data
-Basic information
Entry | Database: PDB / ID: 8.0E+91 | ||||||
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Title | Cryo-EM structure of substrate-free ClpX.ClpP | ||||||
Components |
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Keywords | CHAPERONE / AAA+ protease / ClpXP / substrate-free | ||||||
Function / homology | Function and homology information 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 / proteasomal protein catabolic process / serine-type peptidase activity / proteolysis involved in protein catabolic process ...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 / proteasomal protein catabolic process / serine-type peptidase activity / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / peptidase activity / ATPase binding / response to heat / 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: 2.57 Å | ||||||
Authors | Ghanbarpour, A. / Davis, J.H. / Sauer, R.T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-EM structure of substrate-free DNClpX.ClpP Authors: Ghanbarpour, A. / Cohen, S. / Davis, J.H. / Sauer, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8e91.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8e91.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 8e91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8e91_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8e91_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8e91_validation.xml.gz | 115.9 KB | Display | |
Data in CIF | 8e91_validation.cif.gz | 180.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/8e91 ftp://data.pdbj.org/pub/pdb/validation_reports/e9/8e91 | HTTPS FTP |
-Related structure data
Related structure data | 27952MC 8e7vC 8e8qC M: map data used to model this data C: citing same article (ref.) |
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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: 46414.848 Da / Num. of mol.: 6 / Mutation: K408E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clpX / Production host: Escherichia coli (E. coli) / References: UniProt: C3TLS7 #2: Protein | Mass: 23468.869 Da / Num. of mol.: 14 / Fragment: UNP residues 16-207 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clpP, lopP, b0437, JW0427 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6G7, endopeptidase Clp #3: Chemical | ChemComp-AGS / #4: Chemical | #5: Chemical | 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: ClpXP AAA protease / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | 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 FIELD / Nominal defocus max: 1750 nm / Nominal defocus min: 300 nm / Cs: 2.7 mm |
Image recording | Electron dose: 52.67 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Details: Patch CTF estimation, cryoSPARC / Type: NONE | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 214397 / Details: GSFSC resolution after autotightening / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6WRF Accession code: 6WRF / Source name: PDB / Type: experimental model |