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Yorodumi- PDB-7ypk: Close-ring hexamer of the substrate-bound Lon protease with an S6... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ypk | ||||||
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Title | Close-ring hexamer of the substrate-bound Lon protease with an S678A mutation | ||||||
Components |
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Keywords | HYDROLASE / Lon protease / hydrolysis / AAA proteins | ||||||
Function / homology | Function and homology information endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / cellular response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Meiothermus taiwanensis (bacteria) Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Li, S. / Hsieh, K.Y. / Kuo, C.I. / Lee, S.H. / Ho, M.R. / Wang, C.H. / Zhang, K. / Chang, C.I. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: A 5+1 assemble-to-activate mechanism of the Lon proteolytic machine. Authors: Shanshan Li / Kan-Yen Hsieh / Chiao-I Kuo / Tzu-Chi Lin / Szu-Hui Lee / Yi-Ru Chen / Chun-Hsiung Wang / Meng-Ru Ho / See-Yeun Ting / Kaiming Zhang / Chung-I Chang / Abstract: Many AAA+ (ATPases associated with diverse cellular activities) proteins function as protein or DNA remodelers by threading the substrate through the central pore of their hexameric assemblies. In ...Many AAA+ (ATPases associated with diverse cellular activities) proteins function as protein or DNA remodelers by threading the substrate through the central pore of their hexameric assemblies. In this ATP-dependent translocating state, the substrate is gripped by the pore loops of the ATPase domains arranged in a universal right-handed spiral staircase organization. However, the process by which a AAA+ protein is activated to adopt this substrate-pore-loop arrangement remains unknown. We show here, using cryo-electron microscopy (cryo-EM), that the activation process of the Lon AAA+ protease may involve a pentameric assembly and a substrate-dependent incorporation of the sixth protomer to form the substrate-pore-loop contacts seen in the translocating state. Based on the structural results, we design truncated monomeric mutants that inhibit Lon activity by binding to the native pentamer and demonstrated that expressing these monomeric mutants in Escherichia coli cells containing functional Lon elicits specific phenotypes associated with lon deficiency, including the inhibition of persister cell formation. These findings uncover a substrate-dependent assembly process for the activation of a AAA+ protein and demonstrate a targeted approach to selectively inhibit its function within cells. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ypk.cif.gz | 777.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ypk.ent.gz | 658.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ypk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/7ypk ftp://data.pdbj.org/pub/pdb/validation_reports/yp/7ypk | HTTPS FTP |
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-Related structure data
Related structure data | 34003MC 7yphC 7ypiC 7ypjC 7yuhC 7yumC 7yupC 7yutC 7yuuC 7yuvC 7yuwC 7yuxC 8k3yC 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/peptide | Mass: 1635.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Unfolded substate / Source: (natural) Bos taurus (cattle) | ||||||
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#2: Protein | Mass: 88538.594 Da / Num. of mol.: 6 / Mutation: S678A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Meiothermus taiwanensis (bacteria) / Gene: lonA1, lon, lon1_1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059VAZ3, endopeptidase La #3: Chemical | ChemComp-ADP / Has ligand of interest | Y | Sequence details | The sequence of alpha-S1-casein is corresponded to the UniProt entry P02662. However, the authors ...The sequence of alpha-S1-casein is corresponded to the UniProt entry P02662. However, the authors do not know how the coordinates align with the sequence and the residue numbering is arbitrary. | |
-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: 0.53 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Lon protease was incubated with alpha-S1-casein | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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 FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 2.52 sec. / Electron dose: 59 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 12546 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1756270 | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 207760 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7FID Accession code: 7FID / Source name: PDB / Type: experimental model |