+Open data
-Basic information
Entry | Database: PDB / ID: 7wi4 | ||||||
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Title | Cryo-EM structure of E.Coli FtsH protease cytosolic domains | ||||||
Components | ATP-dependent zinc metalloprotease FtsH | ||||||
Keywords | HYDROLASE / complex / MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information membrane protein complex / plasma membrane protein complex / 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 / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Qiao, Z. / Gao, Y.G. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: Cell Rep / Year: 2022 Title: Cryo-EM structure of the entire FtsH-HflKC AAA protease complex. Authors: Zhu Qiao / Tatsuhiko Yokoyama / Xin-Fu Yan / Ing Tsyr Beh / Jian Shi / Sandip Basak / Yoshinori Akiyama / Yong-Gui Gao / Abstract: The membrane-bound AAA protease FtsH is the key player controlling protein quality in bacteria. Two single-pass membrane proteins, HflK and HflC, interact with FtsH to modulate its proteolytic ...The membrane-bound AAA protease FtsH is the key player controlling protein quality in bacteria. Two single-pass membrane proteins, HflK and HflC, interact with FtsH to modulate its proteolytic activity. Here, we present structure of the entire FtsH-HflKC complex, comprising 12 copies of both HflK and HflC, all of which interact reciprocally to form a cage, as well as four FtsH hexamers with periplasmic domains and transmembrane helices enclosed inside the cage and cytoplasmic domains situated at the base of the cage. FtsH K61/D62/S63 in the β2-β3 loop in the periplasmic domain directly interact with HflK, contributing to complex formation. Pull-down and in vivo enzymatic activity assays validate the importance of the interacting interface for FtsH-HflKC complex formation. Structural comparison with the substrate-bound human m-AAA protease AFG3L2 offers implications for the HflKC cage in modulating substrate access to FtsH. Together, our findings provide a better understanding of FtsH-type AAA protease holoenzyme assembly and regulation. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wi4.cif.gz | 435.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wi4.ent.gz | 353.3 KB | Display | PDB format |
PDBx/mmJSON format | 7wi4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wi4_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7wi4_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7wi4_validation.xml.gz | 74.6 KB | Display | |
Data in CIF | 7wi4_validation.cif.gz | 109 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/7wi4 ftp://data.pdbj.org/pub/pdb/validation_reports/wi/7wi4 | HTTPS FTP |
-Related structure data
Related structure data | 32521MC 7wi3C 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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-Components
#1: Protein | Mass: 70795.055 Da / Num. of mol.: 6 / Mutation: E252Q, E415Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: ftsH, hflB, mrsC, std, tolZ, b3178, JW3145 / Production host: Escherichia coli (E. coli) References: UniProt: P0AAI3, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Chemical | ChemComp-ANP / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-MG / 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: E.Coli protein complex / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.6 mg/ml / 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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32359 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 80 Å2 | ||||||||||||||||||||||||
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