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- EMDB-38077: Cryo-EM structure of ATP-bound FtsE(E163Q)X -

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Basic information

Entry
Database: EMDB / ID: EMD-38077
TitleCryo-EM structure of ATP-bound FtsE(E163Q)X
Map data
Sample
  • Complex: cell division complex FtsEX
    • Protein or peptide: Cell division ATP-binding protein FtsE
    • Protein or peptide: Cell division protein FtsX
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordsabc transporter / cell division / TRANSPORT PROTEIN
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 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
Cell division ATP-binding protein FtsE / Cell division protein FtsX
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsZhang ZY / Chen YT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800052 China
CitationJournal: PLoS Biol / Year: 2024
Title: Structure and activity of the septal peptidoglycan hydrolysis machinery crucial for bacterial cell division.
Authors: Yatian Chen / Jiayue Gu / Biao Yang / Lili Yang / Jie Pang / Qinghua Luo / Yirong Li / Danyang Li / Zixin Deng / Changjiang Dong / Haohao Dong / Zhengyu Zhang /
Abstract: The peptidoglycan (PG) layer is a critical component of the bacterial cell wall and serves as an important target for antibiotics in both gram-negative and gram-positive bacteria. The hydrolysis of ...The peptidoglycan (PG) layer is a critical component of the bacterial cell wall and serves as an important target for antibiotics in both gram-negative and gram-positive bacteria. The hydrolysis of septal PG (sPG) is a crucial step of bacterial cell division, facilitated by FtsEX through an amidase activation system. In this study, we present the cryo-EM structures of Escherichia coli FtsEX and FtsEX-EnvC in the ATP-bound state at resolutions of 3.05 Å and 3.11 Å, respectively. Our PG degradation assays in E. coli reveal that the ATP-bound conformation of FtsEX activates sPG hydrolysis of EnvC-AmiB, whereas EnvC-AmiB alone exhibits autoinhibition. Structural analyses indicate that ATP binding induces conformational changes in FtsEX-EnvC, leading to significant differences from the apo state. Furthermore, PG degradation assays of AmiB mutants confirm that the regulation of AmiB by FtsEX-EnvC is achieved through the interaction between EnvC-AmiB. These findings not only provide structural insight into the mechanism of sPG hydrolysis and bacterial cell division, but also have implications for the development of novel therapeutics targeting drug-resistant bacteria.
History
DepositionNov 20, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38077.png

Downloads & links

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Map

FileDownload / File: emd_38077.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.4515004 - 2.2966208
Average (Standard dev.)-0.000036450525 (±0.022921087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38077_msk_1.map
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Half map: #2

Fileemd_38077_half_map_1.map
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Half map: #1

Fileemd_38077_half_map_2.map
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Sample components

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Entire : cell division complex FtsEX

EntireName: cell division complex FtsEX
Components
  • Complex: cell division complex FtsEX
    • Protein or peptide: Cell division ATP-binding protein FtsE
    • Protein or peptide: Cell division protein FtsX
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: cell division complex FtsEX

SupramoleculeName: cell division complex FtsEX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)

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Macromolecule #1: Cell division ATP-binding protein FtsE

MacromoleculeName: Cell division ATP-binding protein FtsE / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 24.475295 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIRFEHVSKA YLGGRQALQG VTFHMQPGEM AFLTGHSGAG KSTLLKLICG IERPSAGKIW FSGHDITRLK NREVPFLRRQ IGMIFQDHH LLMDRTVYDN VAIPLIIAGA SGDDIRRRVS AALDKVGLLD KAKNFPIQLS GGEQQRVGIA RAVVNKPAVL L ADQPTGNL ...String:
MIRFEHVSKA YLGGRQALQG VTFHMQPGEM AFLTGHSGAG KSTLLKLICG IERPSAGKIW FSGHDITRLK NREVPFLRRQ IGMIFQDHH LLMDRTVYDN VAIPLIIAGA SGDDIRRRVS AALDKVGLLD KAKNFPIQLS GGEQQRVGIA RAVVNKPAVL L ADQPTGNL DDALSEGILR LFEEFNRVGV TVLMATHDIN LISRRSYRML TLSDGHLHGG VGHE

UniProtKB: Cell division ATP-binding protein FtsE

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Macromolecule #2: Cell division protein FtsX

MacromoleculeName: Cell division protein FtsX / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 38.5835 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNKRDAINHI RQFGGRLDRF RKSVGGSGDG GRNAPKRAKS SPKPVNRKTN VFNEQVRYAF HGALQDLKSK PFATFLTVMV IAISLTLPS VCYMVYKNVN QAATQYYPSP QITVYLQKTL DDDAAAGVVA QLQAEQGVEK VNYLSREDAL GEFRNWSGFG G ALDMLEEN ...String:
MNKRDAINHI RQFGGRLDRF RKSVGGSGDG GRNAPKRAKS SPKPVNRKTN VFNEQVRYAF HGALQDLKSK PFATFLTVMV IAISLTLPS VCYMVYKNVN QAATQYYPSP QITVYLQKTL DDDAAAGVVA QLQAEQGVEK VNYLSREDAL GEFRNWSGFG G ALDMLEEN PLPAVAVVIP KLDFQGTESL NTLRDRITQI NGIDEVRMDD SWFARLAALT GLVGRVSAMI GVLMVAAVFL VI GNSVRLS IFARRDSINV QKLIGATDGF ILRPFLYGGA LLGFSGALLS LILSEILVLR LSSAVAEVAQ VFGTKFDING LSF DECLLL LLVCSMIGWV AAWLATVQHL RHFTPE

UniProtKB: Cell division protein FtsX

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 370231
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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