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- EMDB-34668: Cell divisome sPG hydrolysis machinery FtsEX-EnvC -

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Basic information

Entry
Database: EMDB / ID: EMD-34668
TitleCell divisome sPG hydrolysis machinery FtsEX-EnvC
Map data
Sample
  • Complex: Bacterial divisom sPG hydrolysis machinery FtsEX-EnvC
    • Protein or peptide: Cell division ATP-binding protein FtsE
    • Protein or peptide: Cell division protein FtsX
    • Protein or peptide: Murein hydrolase activator EnvC
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordsbacterial cell divison / divisome PG hydrolysis / ABC transporter / Regulator / MEMBRANE PROTEIN
Function / homology
Function and homology information


division septum / divisome complex / peptidoglycan-based cell wall biogenesis / Gram-negative-bacterium-type cell wall / septum digestion after cytokinesis / peptidoglycan turnover / plasma membrane protein complex / FtsZ-dependent cytokinesis / division septum assembly / cell division site ...division septum / divisome complex / peptidoglycan-based cell wall biogenesis / Gram-negative-bacterium-type cell wall / septum digestion after cytokinesis / peptidoglycan turnover / plasma membrane protein complex / FtsZ-dependent cytokinesis / division septum assembly / cell division site / extrinsic component of membrane / ATPase complex / positive regulation of cell division / transmembrane transporter activity / response to radiation / transmembrane transport / metalloendopeptidase activity / outer membrane-bounded periplasmic space / periplasmic space / hydrolase activity / response to xenobiotic stimulus / cell cycle / 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 / Peptidase M23 / Peptidase family M23 / ABC3 transporter permease protein domain / Duplicated hybrid motif ...: / 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 / Murein hydrolase activator EnvC
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsZhang Z / Chen Y
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800052 China
Ministry of Science and Technology (MoST, China)2018YFA093200 China
CitationJournal: To Be Published
Title: Structural insight into the septal peptidoglycan hydrolysis machinery of bacterial cell division
Authors: Zhang Z / Dong H / Chen Y
History
DepositionNov 3, 2022-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateNov 8, 2023-
Current statusNov 8, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34668.png

Downloads & links

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Map

FileDownload / File: emd_34668.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.2753574 - 1.8677766
Average (Standard dev.)-0.00022232762 (±0.012467609)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 483.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34668_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34668_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34668_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Bacterial divisom sPG hydrolysis machinery FtsEX-EnvC

EntireName: Bacterial divisom sPG hydrolysis machinery FtsEX-EnvC
Components
  • Complex: Bacterial divisom sPG hydrolysis machinery FtsEX-EnvC
    • Protein or peptide: Cell division ATP-binding protein FtsE
    • Protein or peptide: Cell division protein FtsX
    • Protein or peptide: Murein hydrolase activator EnvC
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Bacterial divisom sPG hydrolysis machinery FtsEX-EnvC

SupramoleculeName: Bacterial divisom sPG hydrolysis machinery FtsEX-EnvC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Bacterial cell division septal peptidoglycon hydrolysis mechinary complex FtsEX=EnvC
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MG1655
Molecular weightTheoretical: 126 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: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 24.475295 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 (strain K12) (bacteria)
Molecular weightTheoretical: 38.5835 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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: Murein hydrolase activator EnvC

MacromoleculeName: Murein hydrolase activator EnvC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 46.661617 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTRAVKPRRF AIRPIIYASV LSAGVLLCAF SAHADERDQL KSIQADIAAK ERAVRQKQQQ RASLLAQLKK QEEAISEATR KLRETQNTL NQLNKQIDEM NASIAKLEQQ KAAQERSLAA QLDAAFRQGE HTGIQLILSG EESQRGQRLQ AYFGYLNQAR Q ETIAQLKQ ...String:
MTRAVKPRRF AIRPIIYASV LSAGVLLCAF SAHADERDQL KSIQADIAAK ERAVRQKQQQ RASLLAQLKK QEEAISEATR KLRETQNTL NQLNKQIDEM NASIAKLEQQ KAAQERSLAA QLDAAFRQGE HTGIQLILSG EESQRGQRLQ AYFGYLNQAR Q ETIAQLKQ TREEVAMQRA ELEEKQSEQQ TLLYEQRAQQ AKLTQALNER KKTLAGLESS IQQGQQQLSE LRANESRLRN SI ARAEAAA KARAEREARE AQAVRDRQKE ATRKGTTYKP TESEKSLMSR TGGLGAPRGQ AFWPVRGPTL HRYGEQLQGE LRW KGMVIG ASEGTEVKAI ADGRVILADW LQGYGLVVVV EHGKGDMSLY GYNQSALVSV GSQVRAGQPI ALVGSSGGQG RPSL YFEIR RQGQAVNPQP WLGR

UniProtKB: Murein hydrolase activator EnvC

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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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

Concentration1.0 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 30 / Resolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1455436
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8hd0:
Cell divisome sPG hydrolysis machinery FtsEX-EnvC

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