[English] 日本語
Yorodumi
- EMDB-39394: FtsEX in nanodisc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39394
TitleFtsEX in nanodisc
Map data
Sample
  • Complex: FtsEX complex with FtsE-E163Q mutation in nanodisc
    • Protein or peptide: Cell division ATP-binding protein FtsE
    • Protein or peptide: Cell division protein FtsX
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
KeywordsFtsE / FtsX / Gram-negative bacteria / Cell division / MEMBRANE PROTEIN
Function / homology
Function and homology information


division septum / divisome complex / Gram-negative-bacterium-type cell wall / peptidoglycan turnover / plasma membrane protein complex / division septum assembly / FtsZ-dependent cytokinesis / extrinsic component of membrane / cell division site / ATPase complex ...division septum / divisome complex / Gram-negative-bacterium-type cell wall / peptidoglycan turnover / plasma membrane protein complex / division septum assembly / FtsZ-dependent cytokinesis / extrinsic component of membrane / cell division site / ATPase complex / positive regulation of cell division / transmembrane transporter activity / transmembrane transport / cell division / response to antibiotic / ATP hydrolysis activity / ATP binding / membrane / 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 / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. ...: / Cell division protein FtsE, ATP-binding / Cell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain / ABC transporter, lipoprotein release, LolD / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / 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
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsChang S / Dong H / Tang X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000844,31900039 China
CitationJournal: To Be Published
Title: Structural and molecular dynamics simulations reveal the mechanotransduction mechanism of FtsEX
Authors: Chang S / Tang X / Dong H / Chen Y
History
DepositionMar 8, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_39394.png

Downloads & links

-
Map

FileDownload / File: emd_39394.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038
Minimum - Maximum-0.33182457 - 0.8988153
Average (Standard dev.)-0.0005703685 (±0.02165454)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 243.36002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: sharp

Fileemd_39394_additional_1.map
Annotationsharp
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_39394_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_39394_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : FtsEX complex with FtsE-E163Q mutation in nanodisc

EntireName: FtsEX complex with FtsE-E163Q mutation in nanodisc
Components
  • Complex: FtsEX complex with FtsE-E163Q mutation in nanodisc
    • Protein or peptide: Cell division ATP-binding protein FtsE
    • Protein or peptide: Cell division protein FtsX
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE

-
Supramolecule #1: FtsEX complex with FtsE-E163Q mutation in nanodisc

SupramoleculeName: FtsEX complex with FtsE-E163Q mutation in nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli K-12 (bacteria)

-
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 K-12 (bacteria)
Molecular weightTheoretical: 24.575307 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: SGSIRFEHVS KAYLGGRQAL QGVTFHMQPG EMAFLTGHSG AGKSTLLKLI CGIERPSAGK IWFSGHDITR LKNREVPFLR RQIGMIFQD HHLLMDRTVY DNVAIPLIIA GASGDDIRRR VSAALDKVGL LDKAKNFPIQ LSGGEQQRVG IARAVVNKPA V LLADQPTG ...String:
SGSIRFEHVS KAYLGGRQAL QGVTFHMQPG EMAFLTGHSG AGKSTLLKLI CGIERPSAGK IWFSGHDITR LKNREVPFLR RQIGMIFQD HHLLMDRTVY DNVAIPLIIA GASGDDIRRR VSAALDKVGL LDKAKNFPIQ LSGGEQQRVG IARAVVNKPA V LLADQPTG NLDDALSEGI LRLFEEFNRV GVTVLMATHD INLISRRSYR MLTLSDGHLH GGVGHE

UniProtKB: Cell division ATP-binding protein FtsE

-
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 K-12 (bacteria)
Molecular weightTheoretical: 37.852789 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MVTCMEAWAM NKRFRKSVGG SGDGGRNAPK RAKSSPKPVN RKTNVFNEQV RYAFHGALQD LKSKPFATFL TVMVIAISLT LPSVCYMVY KNVNQAATQY YPSPQITVYL QKTLDDDAAA GVVAQLQAEQ GVEKVNYLSR EDALGEFRNW SGFGGALDML E ENPLPAVA ...String:
MVTCMEAWAM NKRFRKSVGG SGDGGRNAPK RAKSSPKPVN RKTNVFNEQV RYAFHGALQD LKSKPFATFL TVMVIAISLT LPSVCYMVY KNVNQAATQY YPSPQITVYL QKTLDDDAAA GVVAQLQAEQ GVEKVNYLSR EDALGEFRNW SGFGGALDML E ENPLPAVA VVIPKLDFQG TESLNTLRDR ITQINGIDEV RMDDSWFARL AALTGLVGRV SAMIGVLMVA AVFLVIGNSV RL SIFARRD SINVQKLIGA TDGFILRPFL YGGALLGFSG ALLSLILSEI LVLRLSSAVA EVAQVFGTKF DINGLSFDEC LLL LLVCSM IGWVAAWLAT VQHLRHFTPE

UniProtKB: Cell division protein FtsX

-
Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

-
Macromolecule #4: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE

MacromoleculeName: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
type: ligand / ID: 4 / Number of copies: 2 / Formula: LPP
Molecular weightTheoretical: 648.891 Da
Chemical component information

ChemComp-LPP:
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 380276
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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