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- EMDB-41761: Cryo-EM structure of Vibrio cholerae FtsE/FtsX/EnvC complex, shortened -

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Basic information

Entry
Database: EMDB / ID: EMD-41761
TitleCryo-EM structure of Vibrio cholerae FtsE/FtsX/EnvC complex, shortened
Map datafull map
Sample
  • Complex: FtsEX
    • Protein or peptide: Cell division ATP-binding protein FtsE
    • Protein or peptide: Cell division protein FtsX
    • Protein or peptide: Peptidase M23
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsmembrane protein / enzyme / TRANSPORT PROTEIN
Function / homology
Function and homology information


cell division / ATP hydrolysis activity / ATP binding / plasma membrane
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 / ABC3 transporter permease protein domain ...: / 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 / ABC3 transporter permease protein domain / Duplicated hybrid motif / 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 / Peptidase M23
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 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_41761.png

Downloads & links

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Map

FileDownload / File: emd_41761.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 450 pix.
= 486. Å		1.08 Å/pix.
x 450 pix.
= 486. Å		1.08 Å/pix.
x 450 pix.
= 486. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.9030028 - 1.5162317
Average (Standard dev.)0.00025122726 (±0.01747153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 486.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41761_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: half map 2

Fileemd_41761_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_41761_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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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: Cell division ATP-binding protein FtsE
    • Protein or peptide: Cell division protein FtsX
    • Protein or peptide: Peptidase M23
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: FtsEX

SupramoleculeName: FtsEX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 200 KDa

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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: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 25.882668 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PALSGGDGVI RFQQVSKAYR GGRQALQKVD FHLRRGEMAF LGGHSGAGKS TLLKLICAIE RPTDGKISFN GHDITRIPNK DIPFLRRNI GIVFQDHRLL MDRSIYDNVA LPMRIESISE NEIKRRVSAA LDKTGLLDKA RCLPSQLSGG EQQRVGIARA V VNRPTLLL ...String:
PALSGGDGVI RFQQVSKAYR GGRQALQKVD FHLRRGEMAF LGGHSGAGKS TLLKLICAIE RPTDGKISFN GHDITRIPNK DIPFLRRNI GIVFQDHRLL MDRSIYDNVA LPMRIESISE NEIKRRVSAA LDKTGLLDKA RCLPSQLSGG EQQRVGIARA V VNRPTLLL ADEPTGNLDP ELSSRVLRLF EEFNRAGVTI LLATHDIHLV NSRPQYRHLE LNQGFLSEVA DYGR

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: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 36.516773 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAVKPGNQKI SKTTKSTKSK PRDVKRAKTD SFLAIHFKQA KASFAALWRR PLGNILTLAV ISMALALPAS LYLLSKNIAS VAERVAEPS QLSVYLHIDT PEPRIIVLKD DLERRDEIAK VKYISPQQGL DDLSQYAGFE QAISLLDNAT LPAVLVVTPK V DSREQIQT ...String:
MAVKPGNQKI SKTTKSTKSK PRDVKRAKTD SFLAIHFKQA KASFAALWRR PLGNILTLAV ISMALALPAS LYLLSKNIAS VAERVAEPS QLSVYLHIDT PEPRIIVLKD DLERRDEIAK VKYISPQQGL DDLSQYAGFE QAISLLDNAT LPAVLVVTPK V DSREQIQT LAKALQAEEG VTDVRMDEDW FARLDAIRHL ATIVVISLSS LMLMSVFLIV GNTLRFNVQA NKEEIQTMKL IG ATDAYIL RPYLYSGMWF GLLGAVAAWL LTALMTILLN GAVEALAQLY DSRFRLIGLG WDESLLLLML GVFLGCVAAK VSA KRHLKE IEPV

UniProtKB: Cell division protein FtsX

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Macromolecule #3: Peptidase M23

MacromoleculeName: Peptidase M23 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 43.410895 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTATDPHAIF SDFLGKTLTH RLLACLLFMV SPSLFAATQQ ELTGVKSEIS RQQQSLAEQQ KSLDQLQQAL KQQELGINSI ENQITKTKN DLENANRNIA QLNSNIQALE TQKQQQADKL ERLLQTYYLT KRSLTNGQFF HRSADEDRIS QYYQHLAKSR A QAIEALEK ...String:
MTATDPHAIF SDFLGKTLTH RLLACLLFMV SPSLFAATQQ ELTGVKSEIS RQQQSLAEQQ KSLDQLQQAL KQQELGINSI ENQITKTKN DLENANRNIA QLNSNIQALE TQKQQQADKL ERLLQTYYLT KRSLTNGQFF HRSADEDRIS QYYQHLAKSR A QAIEALEK TQTELNSNQK QRQTEREQIE KLLAEQTQQR DKLAKTQSER KQTVKKIESS ISGNKTYLAE LQRNETRLKA EI AKAAKRN AVLMNGIASQ RGKLPWPLKG RVLHNFGERQ TGQIDWKGLV IDANYGQEVK AVYPGTIVFA EYLRGYGLVV LLD HGKGDM TLYGFNQTLL KKEGDKVTTG ETIALAGDTG GQSRPALYFE IRRNSRAENP SQWLQR

UniProtKB: Peptidase M23

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*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

Concentration8 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium 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
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2434011
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 179239
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.3)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.3)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 3.3)

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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
Output model

PDB-8tzk:
Cryo-EM structure of Vibrio cholerae FtsE/FtsX/EnvC complex, shortened

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