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- PDB-8idd: Cryo-EM structure of Mycobacterium tuberculosis ATP bound FtsEX/R... -
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Basic information
Entry | Database: PDB / ID: 8idd | ||||||
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Title | Cryo-EM structure of Mycobacterium tuberculosis ATP bound FtsEX/RipC complex in peptidisc | ||||||
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![]() | TRANSPORT PROTEIN / complex | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases) / cell division site / transmembrane transporter activity / cysteine-type peptidase activity / transmembrane transport / manganese ion binding / cell division / magnesium ion binding / ATP hydrolysis activity / proteolysis ...Hydrolases; Acting on peptide bonds (peptidases) / cell division site / transmembrane transporter activity / cysteine-type peptidase activity / transmembrane transport / manganese ion binding / cell division / magnesium ion binding / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
![]() | Li, J. / Xu, X. / Luo, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Regulation of the cell division hydrolase RipC by the FtsEX system in Mycobacterium tuberculosis. Authors: Jianwei Li / Xin Xu / Jian Shi / Juan A Hermoso / Lok-To Sham / Min Luo / ![]() ![]() Abstract: The FtsEX complex regulates, directly or via a protein mediator depending on bacterial genera, peptidoglycan degradation for cell division. In mycobacteria and Gram-positive bacteria, the FtsEX ...The FtsEX complex regulates, directly or via a protein mediator depending on bacterial genera, peptidoglycan degradation for cell division. In mycobacteria and Gram-positive bacteria, the FtsEX system directly activates peptidoglycan-hydrolases by a mechanism that remains unclear. Here we report our investigation of Mycobacterium tuberculosis FtsEX as a non-canonical regulator with high basal ATPase activity. The cryo-EM structures of the FtsEX system alone and in complex with RipC, as well as the ATP-activated state, unveil detailed information on the signal transduction mechanism, leading to the activation of RipC. Our findings indicate that RipC is recognized through a "Match and Fit" mechanism, resulting in an asymmetric rearrangement of the extracellular domains of FtsX and a unique inclined binding mode of RipC. This study provides insights into the molecular mechanisms of FtsEX and RipC regulation in the context of a critical human pathogen, guiding the design of drugs targeting peptidoglycan remodeling. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 212.4 KB | Display | ![]() |
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PDB format | ![]() | 164.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 35364MC ![]() 8idbC ![]() 8idcC ![]() 8igqC ![]() 8jiaC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 25766.697 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: O05779 #2: Protein | Mass: 32851.355 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: A0A045GRS5 #3: Protein | | Mass: 39792.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P9WHU2, Hydrolases; Acting on peptide bonds (peptidases) #4: 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 |
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Sample preparation
Component | Name: complex of FtsEX-RipC-ATP / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Image recording | Average exposure time: 6.02 sec. / Electron dose: 38.837 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111341 / Symmetry type: POINT | ||||||||||||||||||||||||
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