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- PDB-8w6j: Cryo-EM structure of Escherichia coli Str K12 FtsE(E163Q)X/EnvC c... -

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Basic information

Entry
Database: PDB / ID: 8w6j
TitleCryo-EM structure of Escherichia coli Str K12 FtsE(E163Q)X/EnvC complex with ATP in peptidisc
Components
  • Cell division ATP-binding protein FtsE
  • Cell division protein FtsX
  • Murein hydrolase activator EnvC
KeywordsTRANSPORT PROTEIN / complex
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 / division septum assembly / FtsZ-dependent cytokinesis / extrinsic component of membrane ...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 / division septum assembly / FtsZ-dependent cytokinesis / extrinsic component of membrane / cell division site / ATPase complex / positive regulation of cell division / transmembrane transporter activity / response to radiation / metalloendopeptidase activity / transmembrane transport / outer membrane-bounded periplasmic space / periplasmic space / hydrolase activity / response to xenobiotic stimulus / 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 / Peptidase M23 / Peptidase family M23 / 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 / Duplicated hybrid motif / 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 / Cell division ATP-binding protein FtsE / Cell division protein FtsX / Murein hydrolase activator EnvC
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLi, J. / Xu, X. / He, Y. / Luo, M.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)A-0008412-00-00 Singapore
CitationJournal: To Be Published
Title: Cryo-EM structure of Escherichia coli Str K12 FtsE(E163Q)X/EnvC complex with ATP in peptidisc
Authors: Li, J. / Xu, X. / He, Y. / Luo, M.
History
DepositionAug 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Cell division ATP-binding protein FtsE
A: Cell division protein FtsX
C: Cell division protein FtsX
D: Cell division ATP-binding protein FtsE
E: Murein hydrolase activator EnvC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,7947
Polymers172,7795
Non-polymers1,0142
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
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 K-12 (bacteria) / Gene: ftsE
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
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 K-12 (bacteria) / Gene: ftsX
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0AC30
#3: Protein Murein hydrolase activator EnvC


Mass: 46661.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: envC
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P37690
#4: 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
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: ATP bound FtsE(E163Q)X-EnvC complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 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: SPOT SCAN
Electron lensMode: 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 recordingAverage 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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182732 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058705
ELECTRON MICROSCOPYf_angle_d1.14711819
ELECTRON MICROSCOPYf_dihedral_angle_d6.1541217
ELECTRON MICROSCOPYf_chiral_restr0.0581390
ELECTRON MICROSCOPYf_plane_restr0.0061507

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