+Open data
-Basic information
Entry | Database: PDB / ID: 8e8q | ||||||
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Title | Cryo-EM structure of substrate-free DNClpX.ClpP | ||||||
Components |
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Keywords | CHAPERONE / AAA+ protease / ClpXP | ||||||
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: 3.12 Å | ||||||
Authors | Ghanbarpour, A. / Cohen, S. / 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 | 8e8q.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8e8q.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 8e8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8e8q_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8e8q_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8e8q_validation.xml.gz | 116.7 KB | Display | |
Data in CIF | 8e8q_validation.cif.gz | 179.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/8e8q ftp://data.pdbj.org/pub/pdb/validation_reports/e8/8e8q | HTTPS FTP |
-Related structure data
Related structure data | 27946MC 8e7vC 8e91C 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: 42355.812 Da / Num. of mol.: 6 / Fragment: UNP residues 62-424 / Mutation: C169S, K408E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clpX, lopC, b0438, JW0428 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6H1 #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-ATP / #4: Chemical | #5: Chemical | 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: 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: 2500 nm / Nominal defocus min: 250 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Image recording | Electron dose: 49.39 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 2405 |
-Processing
EM software |
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CTF correction | Details: patch CTF estimation / Type: NONE | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 171869 / 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 |