[English] 日本語
Yorodumi
- EMDB-80113: Cryo-EM structure of Pseudomonas aeruginosa FtsQBLWI in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-80113
TitleCryo-EM structure of Pseudomonas aeruginosa FtsQBLWI in complex with imipenem
Map data
Sample
  • Complex: Cryo-EM structure of Pseudomonas aeruginosa FtsQBLWI in complex with imipenem
    • Protein or peptide: Cell division protein FtsQ
    • Protein or peptide: Cell division protein FtsL
    • Protein or peptide: Cell division protein FtsB
    • Protein or peptide: Probable peptidoglycan glycosyltransferase FtsW
    • Protein or peptide: Peptidoglycan D,D-transpeptidase FtsI
  • Ligand: (2~{R},4~{R})-4-(2-methanimidamidoethylsulfanyl)-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid
Keywordscore divisome / peptidoglycan D / D-transpeptidase / imipenem / ANTIBIOTIC
Function / homology
Function and homology information


FtsQBL complex / lipid-linked peptidoglycan transporter activity / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / cell septum / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / FtsZ-dependent cytokinesis / cell division site ...FtsQBL complex / lipid-linked peptidoglycan transporter activity / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / cell septum / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / 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 / Probable peptidoglycan glycosyltransferase FtsW/RodA / Cell cycle protein ...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 / Probable peptidoglycan glycosyltransferase FtsW/RodA / Cell cycle protein / 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 / Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / POTRA domain / POTRA domain profile. / : / 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: 3.6 Å
AuthorsZhu S
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2022YFA1303500 China
CitationJournal: Structure / Year: 2026
Title: Structural, functional, and mechanistic studies of the bacterial divisome FtsWIQBL in complex with antibiotics.
Authors: Shimin Zhu / Yanjie Hu / Rong Wang / Danyang Li / Zhengyu Zhang / Changjiang Dong /
Abstract: Septal peptidoglycan (sPG) biosynthesis during bacterial cell division is driven by the dynamic divisome complex. Its core components, glycosyltransferase FtsW and transpeptidase FtsI are responsible ...Septal peptidoglycan (sPG) biosynthesis during bacterial cell division is driven by the dynamic divisome complex. Its core components, glycosyltransferase FtsW and transpeptidase FtsI are responsible for glycan chain polymerization and crosslinking, respectively. FtsI is also the target of β-lactams. The essential membrane complex FtsQ-FtsB-FtsL regulates FtsWI enzymatic activity. However, the mechanism of FtsQBLWI-mediated sPG synthesis and β-lactam-induced conformational changes have remained elusive. Here, we present cryo-electron microscopy (cryo-EM) structures of the Pseudomonas aeruginosa FtsQBLWI complex in the apo state and bound to aztreonam or imipenem. Our work reveals intricate structural details, including the putative substrate-binding cavities of FtsW, FtsI-mediated allosteric activation of FtsW, and β-lactam-triggered conformational rearrangements. Collectively, these structural, genetic and biochemical analyses reveal the mechanism of FtsQBLWI-controlled sPG synthesis and β-lactam action on this complex, providing a molecular basis for optimizing existing β-lactams and developing novel antibiotics.
History
DepositionApr 3, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_80113.png

Downloads & links

-
Map

FileDownload / File: emd_80113.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.29373953 - 1.2970502
Average (Standard dev.)0.0057529463 (±0.019407855)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Cryo-EM structure of Pseudomonas aeruginosa FtsQBLWI in complex w...

EntireName: Cryo-EM structure of Pseudomonas aeruginosa FtsQBLWI in complex with imipenem
Components
  • Complex: Cryo-EM structure of Pseudomonas aeruginosa FtsQBLWI in complex with imipenem
    • Protein or peptide: Cell division protein FtsQ
    • Protein or peptide: Cell division protein FtsL
    • Protein or peptide: Cell division protein FtsB
    • Protein or peptide: Probable peptidoglycan glycosyltransferase FtsW
    • Protein or peptide: Peptidoglycan D,D-transpeptidase FtsI
  • Ligand: (2~{R},4~{R})-4-(2-methanimidamidoethylsulfanyl)-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid

-
Supramolecule #1: Cryo-EM structure of Pseudomonas aeruginosa FtsQBLWI in complex w...

SupramoleculeName: Cryo-EM structure of Pseudomonas aeruginosa FtsQBLWI in complex with imipenem
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)

-
Macromolecule #1: Cell division protein FtsQ

MacromoleculeName: Cell division protein FtsQ / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 32.290223 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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

-
Macromolecule #2: Cell division protein FtsL

MacromoleculeName: Cell division protein FtsL / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 11.150034 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSRLFVKRLP TGSFLMLLLY IGLLLSAIAV AYSTYWNRQL LNSLYSELSV RDKAQAEWGR LILEQSTWTA HSRIESLAVE QLRMRVPDP AEVRMVAP

UniProtKB: Cell division protein FtsL

-
Macromolecule #3: Cell division protein FtsB

MacromoleculeName: Cell division protein FtsB / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 10.890521 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MRLRSPYWLF VVLILALAGL QYRLWVGDGS LAQVRDLQKQ IADQHGENER LLERNRILEA EVAELKKGTE TVEERARHEL GMVKDGETL YQLAK

UniProtKB: Cell division protein FtsB

-
Macromolecule #4: Probable peptidoglycan glycosyltransferase FtsW

MacromoleculeName: Probable peptidoglycan glycosyltransferase FtsW / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidoglycan glycosyltransferase
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 43.793629 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLSVLRPFPS PLLSRHGIDL DFPLLAGCLA LLGLGLVMVT SASSEVAAAQ SGNPLYFSVR HLIYLVIGLI SCGLTMMVPM ATWQRWGWK LLLVAFGLLV LVITPGIGRE VNGSMRWIGF GLFNIQPSEI AKVCVVIFMA GYLIRRQQEV RESWMGFFKP F VVLLPMAG ...String:
MLSVLRPFPS PLLSRHGIDL DFPLLAGCLA LLGLGLVMVT SASSEVAAAQ SGNPLYFSVR HLIYLVIGLI SCGLTMMVPM ATWQRWGWK LLLVAFGLLV LVITPGIGRE VNGSMRWIGF GLFNIQPSEI AKVCVVIFMA GYLIRRQQEV RESWMGFFKP F VVLLPMAG LLLREPDFGA TVVMMGAAAA MLFLGGVGLF RFGLMVLLAV GAVVLLIQTQ PYRMARLTNF TDPWADQFGA GY QLSQALI AFGRGGWLGM GLGNSIQKQF YLPEAHTDFV FAVLAEELGI VGALATVALF VFVSLRALYI GIWAEQAKQF FSA YVAYGL AFLWIGQFLI NIGVNVGLLP TKGLTLPFLS YGGSSLVICC ACLGMLLRIE WERRTHLGSE EYEFNEEDFA DER

UniProtKB: Probable peptidoglycan glycosyltransferase FtsW

-
Macromolecule #5: Peptidoglycan D,D-transpeptidase FtsI

MacromoleculeName: Peptidoglycan D,D-transpeptidase FtsI / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: serine-type D-Ala-D-Ala carboxypeptidase
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 62.933082 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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

-
Macromolecule #6: (2~{R},4~{R})-4-(2-methanimidamidoethylsulfanyl)-2-[(2~{S},3~{R})...

MacromoleculeName: (2~{R},4~{R})-4-(2-methanimidamidoethylsulfanyl)-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid
type: ligand / ID: 6 / Number of copies: 1 / Formula: A1H3N
Molecular weightTheoretical: 301.362 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS TITAN THEMIS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 238900
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more