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- PDB-8ymc: FtsEX in nanodisc -

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Basic information

Entry
Database: PDB / ID: 8ymc
TitleFtsEX in nanodisc
Components
  • Cell division ATP-binding protein FtsE
  • Cell division protein FtsX
KeywordsMEMBRANE PROTEIN / FtsE / FtsX / Gram-negative bacteria / Cell division
Function / homology
Function and homology information


division septum / divisome complex / Gram-negative-bacterium-type cell wall / peptidoglycan turnover / plasma membrane protein complex / division septum assembly / FtsZ-dependent cytokinesis / extrinsic component of membrane / cell division site / ATPase complex ...division septum / divisome complex / Gram-negative-bacterium-type cell wall / peptidoglycan turnover / plasma membrane protein complex / division septum assembly / FtsZ-dependent cytokinesis / extrinsic component of membrane / cell division site / ATPase complex / positive regulation of cell division / transmembrane transporter activity / transmembrane transport / cell division / response to antibiotic / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Cell division protein FtsE, ATP-binding / Cell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain / ABC transporter, lipoprotein release, LolD / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. ...: / Cell division protein FtsE, ATP-binding / Cell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain / ABC transporter, lipoprotein release, LolD / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chem-LPP / Cell division ATP-binding protein FtsE / Cell division protein FtsX
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsChang, S. / Dong, H. / Tang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000844,31900039 China
CitationJournal: MedComm (2020) / Year: 2024
Title: Structural insights into the mechanotransducing mechanism of FtsEX in cell division.
Authors: Yuejia Chen / Du Guo / Xin Wang / Changbin Zhang / Yatian Chen / Qinghua Luo / Yujiao Chen / Lili Yang / Zhibo Zhang / Tian Hong / Zhengyu Zhang / Haohao Dong / Shenghai Chang / Jianping Hu / Xiaodi Tang /
Abstract: The filamentous temperature-sensitive (Fts) protein FtsEX plays a pivotal role in () cell division by facilitating the activation of peptidoglycan hydrolysis through the adaptor EnvC. FtsEX belongs ...The filamentous temperature-sensitive (Fts) protein FtsEX plays a pivotal role in () cell division by facilitating the activation of peptidoglycan hydrolysis through the adaptor EnvC. FtsEX belongs to the type VII ATP-binding cassette (ABC) transporter superfamily, which harnesses ATP energy to induce mechanical force, triggering a cascade of conformational changes that activate the pathway. However, the precise mechanism by which FtsEX initiates mechanotransmission remains elusive. Due to the inherent instability of this type of ABC transporter protein in vitro, the conformation of FtsEX has solely been determined in the stabilized ATP-bound state. To elucidate the dynamics of FtsEX, we characterized FtsEX and EnvC of various functional structures through cryo-electron microscopy (cryo-EM) and homology modeling. We validated the structures by molecular dynamics simulations. By site-directed mutagenesis and phenotype screening, we also identified the functional residues involved in allosteric communication between FtsE and FtsX as well as FtsX and EnvC. Additionally, we discovered a potential role of phospholipids in stabilizing the complex conformation during mechanotransmission. This comprehensive exploration significantly enhances our understanding of the intricate mechanisms governing bacterial cell division and unveils potential molecular targets for developing innovative antimicrobial drugs to combat antibiotic resistance.
History
DepositionMar 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division ATP-binding protein FtsE
B: Cell division ATP-binding protein FtsE
C: Cell division protein FtsX
D: Cell division protein FtsX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,1688
Polymers124,8564
Non-polymers2,3124
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Cell division ATP-binding protein FtsE


Mass: 24575.307 Da / Num. of mol.: 2 / Mutation: E163Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ftsE, b3463, JW3428
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0A9R7
#2: Protein Cell division protein FtsX


Mass: 37852.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ftsX, ftsS, b3462, JW3427
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0AC30
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H69O8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: FtsEX complex with FtsE-E163Q mutation in nanodisc / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 380276 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028396
ELECTRON MICROSCOPYf_angle_d0.39811366
ELECTRON MICROSCOPYf_dihedral_angle_d6.9351204
ELECTRON MICROSCOPYf_chiral_restr0.0361304
ELECTRON MICROSCOPYf_plane_restr0.0031444

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