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Yorodumi- PDB-8et3: Cryo-EM structure of a delivery complex containing the SspB adapt... -
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-Basic information
Entry | Database: PDB / ID: 8et3 | ||||||
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Title | Cryo-EM structure of a delivery complex containing the SspB adaptor, an ssrA-tagged substrate, and the AAA+ ClpXP protease | ||||||
Components |
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Keywords | CHAPERONE / AAA+ protease / ClpXP / SspB adaptor / HYDROLASE | ||||||
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 / bioluminescence ...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 / bioluminescence / proteolysis involved in protein catabolic process / generation of precursor metabolites and energy / 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: 3.7 Å | ||||||
Authors | Ghanbarpour, A. / Fei, X. / Davis, J.H. / Sauer, R.T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: The SspB adaptor drives structural changes in the AAA+ ClpXP protease during ssrA-tagged substrate delivery. Authors: Alireza Ghanbarpour / Xue Fei / Tania A Baker / Joseph H Davis / Robert T Sauer / Abstract: Energy-dependent protein degradation by the AAA+ ClpXP protease helps maintain protein homeostasis in bacteria and eukaryotic organelles of bacterial origin. In and many other proteobacteria, the ...Energy-dependent protein degradation by the AAA+ ClpXP protease helps maintain protein homeostasis in bacteria and eukaryotic organelles of bacterial origin. In and many other proteobacteria, the SspB adaptor assists ClpXP in degrading ssrA-tagged polypeptides produced as a consequence of tmRNA-mediated ribosome rescue. By tethering these incomplete ssrA-tagged proteins to ClpXP, SspB facilitates their efficient degradation at low substrate concentrations. How this process occurs structurally is unknown. Here, we present a cryo-EM structure of the SspB adaptor bound to a GFP-ssrA substrate and to ClpXP. This structure provides evidence for simultaneous contacts of SspB and ClpX with the ssrA tag within the tethering complex, allowing direct substrate handoff concomitant with the initiation of substrate translocation. Furthermore, our structure reveals that binding of the substrate·adaptor complex induces unexpected conformational changes within the spiral structure of the AAA+ ClpX hexamer and its interaction with the ClpP tetradecamer. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8et3.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8et3.ent.gz | 985.2 KB | Display | PDB format |
PDBx/mmJSON format | 8et3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8et3_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8et3_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8et3_validation.xml.gz | 94.8 KB | Display | |
Data in CIF | 8et3_validation.cif.gz | 147.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/8et3 ftp://data.pdbj.org/pub/pdb/validation_reports/et/8et3 | HTTPS FTP |
-Related structure data
Related structure data | 28585MC 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
-ATP-dependent Clp protease ... , 2 types, 13 molecules ABCDEFHIJKLMN
#1: Protein | Mass: 46414.848 Da / Num. of mol.: 6 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.: 7 / 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 |
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-Protein , 2 types, 3 molecules SYZ
#3: Protein | Mass: 30855.428 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212 |
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#4: Protein | Mass: 18279.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFZ4 |
-Non-polymers , 2 types, 6 molecules
#5: Chemical | ChemComp-AGS / #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 | Name: ClpXP AAA protease complex bound with SspB and GFP-ssrA Type: COMPLEX / Entity ID: #1-#4 / 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 |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / 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: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Image recording | Electron dose: 75.98 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 236728 / 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 |