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- PDB-8hd0: Cell divisome sPG hydrolysis machinery FtsEX-EnvC -

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Basic information

Entry
Database: PDB / ID: 8hd0
TitleCell divisome sPG hydrolysis machinery FtsEX-EnvC
Components
  • Cell division ATP-binding protein FtsE
  • Cell division protein FtsX
  • Murein hydrolase activator EnvC
KeywordsMEMBRANE PROTEIN / bacterial cell divison / divisome PG hydrolysis / ABC transporter / Regulator
Function / homology
Function and homology information


division septum / divisome complex / peptidoglycan-based cell wall biogenesis / Gram-negative-bacterium-type cell wall / septum digestion after cytokinesis / peptidoglycan turnover / plasma membrane protein complex / FtsZ-dependent cytokinesis / division septum assembly / cell division site ...division septum / divisome complex / peptidoglycan-based cell wall biogenesis / Gram-negative-bacterium-type cell wall / septum digestion after cytokinesis / peptidoglycan turnover / plasma membrane protein complex / FtsZ-dependent cytokinesis / division septum assembly / cell division site / extrinsic component of membrane / ATPase complex / positive regulation of cell division / transmembrane transporter activity / response to radiation / transmembrane transport / metalloendopeptidase activity / outer membrane-bounded periplasmic space / periplasmic space / hydrolase activity / response to xenobiotic stimulus / cell cycle / cell division / response to antibiotic / ATP hydrolysis activity / ATP binding / 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 / Peptidase M23 / Peptidase family M23 / ABC3 transporter permease protein domain / Duplicated hybrid motif ...: / Cell division protein FtsE, ATP-binding / Cell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain / ABC transporter, lipoprotein release, LolD / Peptidase M23 / Peptidase family M23 / ABC3 transporter permease protein domain / Duplicated hybrid motif / FtsX-like permease family / 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 / Cell division ATP-binding protein FtsE / Cell division protein FtsX / Murein hydrolase activator EnvC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsZhang, Z. / Chen, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800052 China
Ministry of Science and Technology (MoST, China)2018YFA093200 China
CitationJournal: To Be Published
Title: Structural insight into the septal peptidoglycan hydrolysis machinery of bacterial cell division
Authors: Zhang, Z. / Dong, H. / Chen, Y.
History
DepositionNov 3, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
E: Murein hydrolase activator EnvC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,7947
Polymers172,7795
Non-polymers1,0142
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Cell division ATP-binding protein FtsE


Mass: 24475.295 Da / Num. of mol.: 2 / Mutation: E163Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: ftsE, b3463, JW3428 / Variant: MG1655 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P0A9R7
#2: Protein Cell division protein FtsX /


Mass: 38583.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: ftsX, ftsS, b3462, JW3427 / Variant: MG1655 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P0AC30
#3: Protein Murein hydrolase activator EnvC / Septal ring factor


Mass: 46661.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: envC, yibP, b3613, JW5646 / Variant: MG1655 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P37690
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine 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
Has ligand of interestY

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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: Bacterial divisom sPG hydrolysis machinery FtsEX-EnvC / Type: COMPLEX
Details: Bacterial cell division septal peptidoglycon hydrolysis mechinary complex FtsEX=EnvC
Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.126 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MG1655
Source (recombinant)Organism: Escherichia coli (E. coli) / Cell: C43 / Plasmid: pET28a
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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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 FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
7PHENIXmodel fitting
9PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1455436 / Num. of class averages: 30 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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