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- EMDB-41763: Cryo-EM structure of Vibrio cholerae FtsE Y20A mutant/FtsX/EnvC c... -

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Basic information

Entry
Database: EMDB / ID: EMD-41763
TitleCryo-EM structure of Vibrio cholerae FtsE Y20A mutant/FtsX/EnvC complex
Map datafull map_updated
Sample
  • Complex: FtsEX
    • Protein or peptide: FtsE
Keywordsmembrane protein / enzyme / TRANSPORT PROTEIN
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.37 Å
AuthorsHao A / Lee S-Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)AI166134 United States
CitationJournal: Structure / Year: 2024
Title: Structural insights into the FtsEX-EnvC complex regulation on septal peptidoglycan hydrolysis in Vibrio cholerae.
Authors: Aili Hao / Yang Suo / Seok-Yong Lee /
Abstract: During bacterial cell division, hydrolysis of septal peptidoglycan (sPG) is crucial for cell separation. This sPG hydrolysis is performed by the enzyme amidases whose activity is regulated by the ...During bacterial cell division, hydrolysis of septal peptidoglycan (sPG) is crucial for cell separation. This sPG hydrolysis is performed by the enzyme amidases whose activity is regulated by the integral membrane protein complex FtsEX-EnvC. FtsEX is an ATP-binding cassette transporter, and EnvC is a long coiled-coil protein that interacts with and activates the amidases. The molecular mechanism by which the FtsEX-EnvC complex activates amidases remains largely unclear. We present the cryo-electron microscopy structure of the FtsEX-EnvC complex from the pathogenic bacteria V. cholerae (FtsEX-EnvC). FtsEX-EnvC in the presence of ADP adopts a distinct conformation where EnvC is "horizontally extended" rather than "vertically extended". Subsequent structural studies suggest that EnvC can swing between these conformations in space in a nucleotide-dependent manner. Our structural analysis and functional studies suggest that FtsEX-EnvC employs spatial control of EnvC for amidase activation, providing mechanistic insights into the FtsEX-EnvC regulation on septal peptidoglycan hydrolysis.
History
DepositionAug 27, 2023-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41763.png

Downloads & links

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Map

FileDownload / File: emd_41763.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map_updated
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.18566102 - 1.016874
Average (Standard dev.)0.0009838716 (±0.012158031)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 552.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41763_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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Half map: half map B updated

Fileemd_41763_half_map_1.map
Annotationhalf map B_updated
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A updated

Fileemd_41763_half_map_2.map
Annotationhalf map A_updated
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FtsEX

EntireName: FtsEX
Components
  • Complex: FtsEX
    • Protein or peptide: FtsE

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Supramolecule #1: FtsEX

SupramoleculeName: FtsEX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: FtsE

MacromoleculeName: FtsE / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Vibrio cholerae (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PALSGGDGVI RFQQVSKAYR GGRQALQKVD FHLRRGEMAF LGGHSGAGKS TLLKLICAIE RPTDGKISFN GHDITRIPNK DIPFLRRNIG IVFQDHRLLM DRSIYDNVAL PMRIESISEN EIKRRVSAAL DKTGLLDKAR CLPSQLSGGE QQRVGIARAV VNRPTLLLAD ...String:
PALSGGDGVI RFQQVSKAYR GGRQALQKVD FHLRRGEMAF LGGHSGAGKS TLLKLICAIE RPTDGKISFN GHDITRIPNK DIPFLRRNIG IVFQDHRLLM DRSIYDNVAL PMRIESISEN EIKRRVSAAL DKTGLLDKAR CLPSQLSGGE QQRVGIARAV VNRPTLLLAD EPTGNLDPEL SSRVLRLFEE FNRAGVTILL ATHDIHLVNS RPQYRHLELN QGFLSEVADY GR

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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

Concentration8 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
20.0 mMTris
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Average exposure time: 2.4 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2434011
Startup modelType of model: OTHER
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.3)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 3.3)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.3)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 301853

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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