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- EMDB-39394: FtsEX in nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-39394
TitleFtsEX in nanodisc
Map data
Sample
  • Complex: FtsEX complex with FtsE-E163Q mutation in nanodisc
    • Protein or peptide: Cell division ATP-binding protein FtsE
    • Protein or peptide: Cell division protein FtsX
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
KeywordsFtsE / FtsX / Gram-negative bacteria / Cell division / MEMBRANE 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 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
Cell division ATP-binding protein FtsE / Cell division protein FtsX
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsChang S / Dong H / Tang X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000844,31900039 China
CitationJournal: To Be Published
Title: Structural and molecular dynamics simulations reveal the mechanotransduction mechanism of FtsEX
Authors: Chang S / Tang X / Dong H / Chen Y
History
DepositionMar 8, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39394.png

Downloads & links

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Map

FileDownload / File: emd_39394.map.gz / Format: CCP4 / Size: 52.7 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.)
1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038
Minimum - Maximum-0.33182457 - 0.8988153
Average (Standard dev.)-0.0005703685 (±0.02165454)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 243.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharp

Fileemd_39394_additional_1.map
Annotationsharp
Projections & Slices
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Half map: #1

Fileemd_39394_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_39394_half_map_2.map
Projections & Slices
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Sample components

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Entire : FtsEX complex with FtsE-E163Q mutation in nanodisc

EntireName: FtsEX complex with FtsE-E163Q mutation in nanodisc
Components
  • Complex: FtsEX complex with FtsE-E163Q mutation in nanodisc
    • Protein or peptide: Cell division ATP-binding protein FtsE
    • Protein or peptide: Cell division protein FtsX
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE

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Supramolecule #1: FtsEX complex with FtsE-E163Q mutation in nanodisc

SupramoleculeName: FtsEX complex with FtsE-E163Q mutation in nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli K-12 (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: 24.575307 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: SGSIRFEHVS KAYLGGRQAL QGVTFHMQPG EMAFLTGHSG AGKSTLLKLI CGIERPSAGK IWFSGHDITR LKNREVPFLR RQIGMIFQD HHLLMDRTVY DNVAIPLIIA GASGDDIRRR VSAALDKVGL LDKAKNFPIQ LSGGEQQRVG IARAVVNKPA V LLADQPTG ...String:
SGSIRFEHVS KAYLGGRQAL QGVTFHMQPG EMAFLTGHSG AGKSTLLKLI CGIERPSAGK IWFSGHDITR LKNREVPFLR RQIGMIFQD HHLLMDRTVY DNVAIPLIIA GASGDDIRRR VSAALDKVGL LDKAKNFPIQ LSGGEQQRVG IARAVVNKPA V LLADQPTG NLDDALSEGI LRLFEEFNRV GVTVLMATHD INLISRRSYR MLTLSDGHLH GGVGHE

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: 37.852789 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MVTCMEAWAM NKRFRKSVGG SGDGGRNAPK RAKSSPKPVN RKTNVFNEQV RYAFHGALQD LKSKPFATFL TVMVIAISLT LPSVCYMVY KNVNQAATQY YPSPQITVYL QKTLDDDAAA GVVAQLQAEQ GVEKVNYLSR EDALGEFRNW SGFGGALDML E ENPLPAVA ...String:
MVTCMEAWAM NKRFRKSVGG SGDGGRNAPK RAKSSPKPVN RKTNVFNEQV RYAFHGALQD LKSKPFATFL TVMVIAISLT LPSVCYMVY KNVNQAATQY YPSPQITVYL QKTLDDDAAA GVVAQLQAEQ GVEKVNYLSR EDALGEFRNW SGFGGALDML E ENPLPAVA VVIPKLDFQG TESLNTLRDR ITQINGIDEV RMDDSWFARL AALTGLVGRV SAMIGVLMVA AVFLVIGNSV RL SIFARRD SINVQKLIGA TDGFILRPFL YGGALLGFSG ALLSLILSEI LVLRLSSAVA EVAQVFGTKF DINGLSFDEC LLL LLVCSM IGWVAAWLAT VQHLRHFTPE

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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Macromolecule #4: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE

MacromoleculeName: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
type: ligand / ID: 4 / Number of copies: 2 / Formula: LPP
Molecular weightTheoretical: 648.891 Da
Chemical component information

ChemComp-LPP:
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 380276
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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