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- PDB-8w6i: Cryo-EM structure of Escherichia coli Str K12 FtsEX complex with ... -

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Basic information

Entry
Database: PDB / ID: 8w6i
TitleCryo-EM structure of Escherichia coli Str K12 FtsEX complex with ATP-gamma-S in peptidisc
Components
  • Cell division ATP-binding protein FtsE
  • Cell division protein FtsX
KeywordsTRANSPORT PROTEIN / complex
Function / homology
Function and homology information


division septum / divisome complex / Gram-negative-bacterium-type cell wall / peptidoglycan turnover / plasma membrane protein complex / FtsZ-dependent cytokinesis / division septum assembly / extrinsic component of membrane / ATPase complex / cell division site ...division septum / divisome complex / Gram-negative-bacterium-type cell wall / peptidoglycan turnover / plasma membrane protein complex / FtsZ-dependent cytokinesis / division septum assembly / extrinsic component of membrane / ATPase complex / cell division site / positive regulation of cell division / transmembrane transporter activity / transmembrane transport / 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 / ABC3 transporter permease protein domain / FtsX-like permease family / 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 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / 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: 3.7 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 FtsEX complex with ATP-gamma-S 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
C: Cell division protein FtsX
D: Cell division ATP-binding protein FtsE
A: Cell division protein FtsX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,1666
Polymers126,1204
Non-polymers1,0462
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: 24476.279 Da / Num. of mol.: 2
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: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*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: complex of FtsEX / 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: 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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 116651 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047894
ELECTRON MICROSCOPYf_angle_d1.08210734
ELECTRON MICROSCOPYf_dihedral_angle_d6.8921110
ELECTRON MICROSCOPYf_chiral_restr0.0561273
ELECTRON MICROSCOPYf_plane_restr0.0071365

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