[English] 日本語
Yorodumi
- EMDB-17356: Structure of divisome complex FtsWIQLB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17356
TitleStructure of divisome complex FtsWIQLB
Map data
Sample
  • Complex: divisome complex FtsWIQLB
    • Protein or peptide: Cell division protein FtsL
    • Protein or peptide: Probable peptidoglycan glycosyltransferase FtsW
    • Protein or peptide: Peptidoglycan D,D-transpeptidase FtsI
    • Protein or peptide: Cell division protein FtsB
    • Protein or peptide: Cell division protein FtsQ
KeywordsFtsWIQLB / Gram-negative bacteria / membrane protein / divisome / CELL CYCLE
Function / homology
Function and homology information


cell septum assembly / lipid-linked peptidoglycan transporter activity / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / cell septum / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / cell division site ...cell septum assembly / lipid-linked peptidoglycan transporter activity / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / cell septum / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / 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, C-terminal / Cell division protein FtsQ ...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, C-terminal / Cell division protein FtsQ / 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 speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYang L / Chang S / Tang D / Dong H / Xie T / Luo B / Lu G / Zhu X / Wei X / Dong C ...Yang L / Chang S / Tang D / Dong H / Xie T / Luo B / Lu G / Zhu X / Wei X / Dong C / Zhou R / Zhang X / Tang X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900039,32000844,81971974 China
CitationJournal: Cell Discov / Year: 2024
Title: Structural insights into the activation of the divisome complex FtsWIQLB.
Authors: Lili Yang / Yujiao Chen / Shenghai Chang / Chongrong Shen / Xin Wang / Changbin Zhang / Zhibo Zhang / Bi-Sen Ding / Zhaoming Su / Haohao Dong / Xiaodi Tang /
History
DepositionMay 12, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17356.png

Downloads & links

-
Map

FileDownload / File: emd_17356.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.93 Å
Density
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-1.530756 - 2.220929
Average (Standard dev.)0.00007202665 (±0.032425076)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_17356_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_17356_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : divisome complex FtsWIQLB

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

-
Supramolecule #1: divisome complex FtsWIQLB

SupramoleculeName: divisome complex FtsWIQLB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli K-12 (bacteria)

-
Macromolecule #1: Cell division protein FtsL

MacromoleculeName: Cell division protein FtsL / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 11.150034 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MSRLFVKRLP TGSFLMLLLY IGLLLSAIAV AYSTYWNRQL LNSLYSELSV RDKAQAEWGR LILEQSTWTA HSRIESLAVE QLRMRVPDP AEVRMVAP

UniProtKB: Cell division protein FtsL

-
Macromolecule #2: Probable peptidoglycan glycosyltransferase FtsW

MacromoleculeName: Probable peptidoglycan glycosyltransferase FtsW / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidoglycan glycosyltransferase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 43.793629 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (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 #3: Peptidoglycan D,D-transpeptidase FtsI

MacromoleculeName: Peptidoglycan D,D-transpeptidase FtsI / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: serine-type D-Ala-D-Ala carboxypeptidase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 62.933082 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (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 #4: Cell division protein FtsB

MacromoleculeName: Cell division protein FtsB / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 10.890521 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MRLRSPYWLF VVLILALAGL QYRLWVGDGS LAQVRDLQKQ IADQHGENER LLERNRILEA EVAELKKGTE TVEERARHEL GMVKDGETL YQLAK

UniProtKB: Cell division protein FtsB

-
Macromolecule #5: Cell division protein FtsQ

MacromoleculeName: Cell division protein FtsQ / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 32.290223 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 340758
FSC plot (resolution estimation)

+
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