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- EMDB-16042: Core divisome complex FtsWIQBL from Pseudomonas aeruginosa -

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Basic information

Entry
Database: EMDB / ID: EMD-16042
TitleCore divisome complex FtsWIQBL from Pseudomonas aeruginosa
Map data
Sample
  • Complex: FtsWIQBL
    • Protein or peptide: Probable peptidoglycan glycosyltransferase FtsW
    • Protein or peptide: Peptidoglycan D,D-transpeptidase FtsI
    • Protein or peptide: Cell division protein FtsQ
    • Protein or peptide: Cell division protein FtsL
    • Protein or peptide: Cell division protein FtsB
Keywordsbacterial cell division / peptidoglycan synthesis / membrane protein complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


lipid-linked peptidoglycan transporter activity / cell septum assembly / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / cell septum / serine-type D-Ala-D-Ala carboxypeptidase / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / FtsZ-dependent cytokinesis / cell division site ...lipid-linked peptidoglycan transporter activity / cell septum assembly / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / cell septum / serine-type D-Ala-D-Ala carboxypeptidase / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / FtsZ-dependent cytokinesis / cell division site / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / proteolysis / plasma membrane
Similarity search - Function
Probable peptidoglycan glycosyltransferase FtsW / Cell division protein FtsL / Cell division protein FtsL / Cell cycle, FtsW / RodA / SpoVE, conserved site / Cell cycle proteins ftsW / rodA / spoVE signature. / Septum formation initiator FtsL/DivIC / Cell division protein FtsB / Septum formation initiator / Cell division protein FtsQ / Cell division protein FtsQ, C-terminal ...Probable peptidoglycan glycosyltransferase FtsW / Cell division protein FtsL / Cell division protein FtsL / Cell cycle, FtsW / RodA / SpoVE, conserved site / Cell cycle proteins ftsW / rodA / spoVE signature. / Septum formation initiator FtsL/DivIC / Cell division protein FtsB / Septum formation initiator / Cell division protein FtsQ / Cell division protein FtsQ, C-terminal / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Probable peptidoglycan glycosyltransferase FtsW/RodA / Cell cycle protein / Peptidoglycan D,D-transpeptidase FtsI / POTRA domain / POTRA domain profile. / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Peptidoglycan D,D-transpeptidase FtsI / Cell division protein FtsQ / Cell division protein FtsL / Probable peptidoglycan glycosyltransferase FtsW / Cell division protein FtsB
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsKaeshammer L / van den Ent F / Jeffery M / Lowe J
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
Citation
Journal: Nat Microbiol / Year: 2023
Title: Cryo-EM structure of the bacterial divisome core complex and antibiotic target FtsWIQBL.
Authors: Lisa Käshammer / Fusinita van den Ent / Magnus Jeffery / Nicolas L Jean / Victoria L Hale / Jan Löwe /
Abstract: In most bacteria, cell division relies on the synthesis of new cell wall material by the multiprotein divisome complex. Thus, at the core of the divisome are the transglycosylase FtsW, which ...In most bacteria, cell division relies on the synthesis of new cell wall material by the multiprotein divisome complex. Thus, at the core of the divisome are the transglycosylase FtsW, which synthesises peptidoglycan strands from its substrate Lipid II, and the transpeptidase FtsI that cross-links these strands to form a mesh, shaping and protecting the bacterial cell. The FtsQ-FtsB-FtsL trimeric complex interacts with the FtsWI complex and is involved in regulating its enzymatic activities; however, the structure of this pentameric complex is unknown. Here, we present the cryogenic electron microscopy structure of the FtsWIQBL complex from Pseudomonas aeruginosa at 3.7 Å resolution. Our work reveals intricate structural details, including an extended coiled coil formed by FtsL and FtsB and the periplasmic interaction site between FtsL and FtsI. Our structure explains the consequences of previously reported mutations and we postulate a possible activation mechanism involving a large conformational change in the periplasmic domain. As FtsWIQBL is central to the divisome, our structure is foundational for the design of future experiments elucidating the precise mechanism of bacterial cell division, an important antibiotic target.
#2: Journal: Biorxiv / Year: 2022
Title: Divisome core complex in bacterial cell division revealed by cryo-EM
Authors: Kashammer L / van den Ent F / Jeffery M / Jean NL / Hale VL / Lowe J
History
DepositionOct 28, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16042.png

Downloads & links

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Map

FileDownload / File: emd_16042.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 280 pix.
= 294. Å		1.05 Å/pix.
x 280 pix.
= 294. Å		1.05 Å/pix.
x 280 pix.
= 294. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.031094668 - 0.069077246
Average (Standard dev.)0.00004738906 (±0.0014115719)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 294.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_16042_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16042_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : FtsWIQBL

EntireName: FtsWIQBL
Components
  • Complex: FtsWIQBL
    • Protein or peptide: Probable peptidoglycan glycosyltransferase FtsW
    • Protein or peptide: Peptidoglycan D,D-transpeptidase FtsI
    • Protein or peptide: Cell division protein FtsQ
    • Protein or peptide: Cell division protein FtsL
    • Protein or peptide: Cell division protein FtsB

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Supramolecule #1: FtsWIQBL

SupramoleculeName: FtsWIQBL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 164 KDa

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Macromolecule #1: Probable peptidoglycan glycosyltransferase FtsW

MacromoleculeName: Probable peptidoglycan glycosyltransferase FtsW / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidoglycan glycosyltransferase
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Molecular weightTheoretical: 48.24143 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTAWSHPQFE KGSAGSAAGS GAGWSHPQFE KGLEVLFQGP GGSSMLSVLR PFPSPLLSRH GIDLDFPLLA GCLALLGLGL VMVTSASSE VAAAQSGNPL YFSVRHLIYL VIGLISCGLT MMVPMATWQR WGWKLLLVAF GLLVLVITPG IGREVNGSMR W IGFGLFNI ...String:
MTAWSHPQFE KGSAGSAAGS GAGWSHPQFE KGLEVLFQGP GGSSMLSVLR PFPSPLLSRH GIDLDFPLLA GCLALLGLGL VMVTSASSE VAAAQSGNPL YFSVRHLIYL VIGLISCGLT MMVPMATWQR WGWKLLLVAF GLLVLVITPG IGREVNGSMR W IGFGLFNI QPSEIAKVCV VIFMAGYLIR RQQEVRESWM GFFKPFVVLL PMAGLLLREP DFGATVVMMG AAAAMLFLGG VG LFRFGLM VLLAVGAVVL LIQTQPYRMA RLTNFTDPWA DQFGAGYQLS QALIAFGRGG WLGMGLGNSI QKQFYLPEAH TDF VFAVLA EELGIVGALA TVALFVFVSL RALYIGIWAE QAKQFFSAYV AYGLAFLWIG QFLINIGVNV GLLPTKGLTL PFLS YGGSS LVICCACLGM LLRIEWERRT HLGSEEYEFN EEDFADER

UniProtKB: Probable peptidoglycan glycosyltransferase FtsW

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Macromolecule #2: Peptidoglycan D,D-transpeptidase FtsI

MacromoleculeName: Peptidoglycan D,D-transpeptidase FtsI / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: serine-type D-Ala-D-Ala carboxypeptidase
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Molecular weightTheoretical: 62.933082 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKLNYFQGAL YPWRFCVIVG LLLAMVGAIV WRIVDLHVID HDFLKGQGDA RSVRHIAIPA HRGLITDRNG EPLAVSTPVT TLWANPKEL MTAKERWPQL AAALGQDTKL FADRIEQNAE REFIYLVRGL TPEQGEGVIA LKVPGVYSIE EFRRFYPAGE V VAHAVGFT ...String:
MKLNYFQGAL YPWRFCVIVG LLLAMVGAIV WRIVDLHVID HDFLKGQGDA RSVRHIAIPA HRGLITDRNG EPLAVSTPVT TLWANPKEL MTAKERWPQL AAALGQDTKL FADRIEQNAE REFIYLVRGL TPEQGEGVIA LKVPGVYSIE EFRRFYPAGE V VAHAVGFT DVDDRGREGI ELAFDEWLAG VPGKRQVLKD RRGRVIKDVQ VTKNAKPGKT LALSIDLRLQ YLAHRELRNA LL ENGAKAG SLVIMDVKTG EILAMTNQPT YNPNNRRNLQ PAAMRNRAMI DVFEPGSTVK PFSMSAALAS GRWKPSDIVD VYP GTLQIG RYTIRDVSRN SRQLDLTGIL IKSSNVGISK IAFDIGAESI YSVMQQVGLG QDTGLGFPGE RVGNLPNHRK WPKA ETATL AYGYGLSVTA IQLAHAYAAL ANDGKSVPLS MTRVDRVPDG VQVISPEVAS TVQGMLQQVV EAQGGVFRAQ VPGYH AAGK SGTARKVSVG TKGYRENAYR SLFAGFAPAT DPRIAMVVVI DEPSKAGYFG GLVSAPVFSK VMAGALRLMN VPPDNL PTA TEQQQVNAAP AKGGRG

UniProtKB: Peptidoglycan D,D-transpeptidase FtsI

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Macromolecule #3: Cell division protein FtsQ

MacromoleculeName: Cell division protein FtsQ / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Molecular weightTheoretical: 32.290223 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNGVLLRHQQ PGGLGRAPRK PMPRGASRLV AKEPLSVRLP KADFSFLKYL AWPLLLAVLG YGAYRGAEYI LPYADRPIAK VSVEGDLSY ISQRAVQQRI SPYLAASFFT IDLAGMRGQL EQMPWIAHAE VRRVWPDQVV IRLDEQLPIA RWGDEALLNN Q GQAFTPKE ...String:
MNGVLLRHQQ PGGLGRAPRK PMPRGASRLV AKEPLSVRLP KADFSFLKYL AWPLLLAVLG YGAYRGAEYI LPYADRPIAK VSVEGDLSY ISQRAVQQRI SPYLAASFFT IDLAGMRGQL EQMPWIAHAE VRRVWPDQVV IRLDEQLPIA RWGDEALLNN Q GQAFTPKE LANYEHLPRL HGPQRAQQQV MQQYQLLSQL LRPLGFSIAR LEMSDRGGWA LTTAQGVEIQ IGRDHVVDKI RR FVSIYDK ALKDQISNIA RIDLRYPNGL AVAWREPVTP ATVATASAVQ

UniProtKB: Cell division protein FtsQ

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Macromolecule #4: Cell division protein FtsL

MacromoleculeName: Cell division protein FtsL / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Molecular weightTheoretical: 11.150034 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSRLFVKRLP TGSFLMLLLY IGLLLSAIAV AYSTYWNRQL LNSLYSELSV RDKAQAEWGR LILEQSTWTA HSRIESLAVE QLRMRVPDP AEVRMVAP

UniProtKB: Cell division protein FtsL

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Macromolecule #5: Cell division protein FtsB

MacromoleculeName: Cell division protein FtsB / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Molecular weightTheoretical: 12.295922 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MRLRSPYWLF VVLILALAGL QYRLWVGDGS LAQVRDLQKQ IADQHGENER LLERNRILEA EVAELKKGTE TVEERARHEL GMVKDGETL YQLAKGGSSG GSSHHHHHH

UniProtKB: Cell division protein FtsB

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136364
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)

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