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Yorodumi- PDB-7tdo: Cryo-EM structure of transmembrane AAA+ protease FtsH in the ADP state -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tdo | ||||||
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Title | Cryo-EM structure of transmembrane AAA+ protease FtsH in the ADP state | ||||||
Components | ATP-dependent zinc metalloprotease FtsH | ||||||
Keywords | HYDROLASE / AAA+ ATPase / protease / hexamer / ADP-bound state | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein catabolic process / metalloendopeptidase activity / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å | ||||||
Authors | Liu, W. / Schoonen, M. / Wang, T. / McSweeney, S. / Liu, Q. | ||||||
Funding support | United States, 1items
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Citation | Journal: Commun Biol / Year: 2022 Title: Cryo-EM structure of transmembrane AAA+ protease FtsH in the ADP state. Authors: Wu Liu / Martien Schoonen / Tong Wang / Sean McSweeney / Qun Liu / Abstract: AAA+ proteases regulate numerous physiological and cellular processes through tightly regulated proteolytic cleavage of protein substrates driven by ATP hydrolysis. FtsH is the only known family of ...AAA+ proteases regulate numerous physiological and cellular processes through tightly regulated proteolytic cleavage of protein substrates driven by ATP hydrolysis. FtsH is the only known family of membrane-anchored AAA+ proteases essential for membrane protein quality control. Although a spiral staircase rotation mechanism for substrate translocation across the FtsH pore has been proposed, the detailed conformational changes among various states have not been clear due to absence of FtsH structures in these states. We report here the cryo-EM structure for Thermotoga maritima FtsH (TmFtsH) in a fully ADP-bound symmetric state. Comparisons of the ADP-state structure with its apo-state and a substrate-engaged yeast YME1 structure show conformational changes in the ATPase domains, rather than the protease domains. A reconstruction of the full-length TmFtsH provides structural insights for the dynamic transmembrane and the periplasmic domains. Our structural analyses expand the understanding of conformational switches between different nucleotide states in ATP hydrolysis by FtsH. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tdo.cif.gz | 511.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tdo.ent.gz | 345.9 KB | Display | PDB format |
PDBx/mmJSON format | 7tdo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tdo_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7tdo_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7tdo_validation.xml.gz | 68.9 KB | Display | |
Data in CIF | 7tdo_validation.cif.gz | 102.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/7tdo ftp://data.pdbj.org/pub/pdb/validation_reports/td/7tdo | HTTPS FTP |
-Related structure data
Related structure data | 25837MC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 68489.664 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: ftsH, TM_0580 / Production host: Escherichia coli (E. coli) References: UniProt: Q9WZ49, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Chemical | ChemComp-ADP / 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: Hexameric FtsH in the ADP-bound state / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Thermotoga maritima (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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: 700 nm |
Image recording | Electron dose: 65 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86652 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 3.66 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS |
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