[English] 日本語
Yorodumi
- EMDB-54965: Polysaccharide co-polymerase FepE open 7 subunit complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54965
TitlePolysaccharide co-polymerase FepE open 7 subunit complex
Map dataPolysaccharide co-polymerase FepE 7 subunit complex from E. coli. Main map
Sample
  • Complex: Open 7 subunit bacterial polysaccharide co-polymerase complex
    • Protein or peptide: Ferric enterobactin transport protein FepE
Keywordsmembrane protein / enzyme / polysaccharide / co-polymerase
Function / homologyferric-enterobactin transmembrane transporter activity / ferric-enterobactin import into cell / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / : / protein tyrosine kinase activity / plasma membrane / Ferric enterobactin transport protein FepE
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWiseman B / Hogbom M
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Swedish Research Council2021-043992 Sweden
Knut and Alice Wallenberg Foundation2023.0201 Sweden
CitationJournal: Research (Wash D C) / Year: 2026
Title: Structural Basis of Lipopolysaccharide O-Antigen Chain Length Modality.
Authors: Benjamin Wiseman / Göran Widmalm / Martin Högbom /
Abstract: Lipopolysaccharides are important components of the gram-negative bacterial cell envelope that are involved in immune evasion and act as a protective barrier. Employing cryo-electron microscopy, we ...Lipopolysaccharides are important components of the gram-negative bacterial cell envelope that are involved in immune evasion and act as a protective barrier. Employing cryo-electron microscopy, we resolved the structure and dynamics of FepE, the copolymerase component of the Wzy-dependent pathway, responsible for the length modulation of very long O-antigen molecules. Comparison of the interior volumes of related copolymerases' periplasmic domains with the volume of hydrated sugars suggests that the size of the periplasmic domain controls the length of the O-antigen, implying that polysaccharide chain polymerization occurs inside the copolymerase periplasmic domain. Moreover, we show the opening of the FepE complex as well as other large mechanistically relevant movements. The opening of the complex presents an attractive corridor for the release of completed polysaccharide chains.
History
DepositionSep 2, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_54965.png

Downloads & links

-
Map

FileDownload / File: emd_54965.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPolysaccharide co-polymerase FepE 7 subunit complex from E. coli. Main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 450 pix.
= 372.6 Å		0.83 Å/pix.
x 450 pix.
= 372.6 Å		0.83 Å/pix.
x 450 pix.
= 372.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.22775328 - 0.46238714
Average (Standard dev.)0.0007989291 (±0.010496945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 372.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Polysaccharide co-polymerase FepE 7 subunit complex from E....

Fileemd_54965_additional_1.map
AnnotationPolysaccharide co-polymerase FepE 7 subunit complex from E. coli. Sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Polysaccharide co-polymerase FepE 7 subunit complex from E....

Fileemd_54965_half_map_1.map
AnnotationPolysaccharide co-polymerase FepE 7 subunit complex from E. coli. Half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Polysaccharide co-polymerase FepE 7 subunit complex from E....

Fileemd_54965_half_map_2.map
AnnotationPolysaccharide co-polymerase FepE 7 subunit complex from E. coli. Half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Open 7 subunit bacterial polysaccharide co-polymerase complex

EntireName: Open 7 subunit bacterial polysaccharide co-polymerase complex
Components
  • Complex: Open 7 subunit bacterial polysaccharide co-polymerase complex
    • Protein or peptide: Ferric enterobactin transport protein FepE

-
Supramolecule #1: Open 7 subunit bacterial polysaccharide co-polymerase complex

SupramoleculeName: Open 7 subunit bacterial polysaccharide co-polymerase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 300 KDa

-
Macromolecule #1: Ferric enterobactin transport protein FepE

MacromoleculeName: Ferric enterobactin transport protein FepE / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 44.029422 KDa
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (bacteria)
SequenceString: MSSLNIKQGS DAHFPDYPLA SPSNNEIDLL NLISVLWRAK KTVMAVVFAF ACAGLLISFI LPQKWTSAAV VTPPEPVQWQ ELEKSFTKL RVLDLDIKID RTEAFNLFIK KFQSVSLLEE YLRSSPYVMD QLKEAKIDEL DLHRAIVALS EKMKAVDDNA S KKKDEPSL ...String:
MSSLNIKQGS DAHFPDYPLA SPSNNEIDLL NLISVLWRAK KTVMAVVFAF ACAGLLISFI LPQKWTSAAV VTPPEPVQWQ ELEKSFTKL RVLDLDIKID RTEAFNLFIK KFQSVSLLEE YLRSSPYVMD QLKEAKIDEL DLHRAIVALS EKMKAVDDNA S KKKDEPSL YTSWTLSFTA PTSEEAQTVL SGYIDYISTL VVKESLENVR NKLEIKTQFE KEKLAQDRIK TKNQLDANIQ RL NYSLDIA NAAGIKKPVY SNGQAVKDDP DFSISLGADG IERKLEIEKA VTDVAELNGE LRNRQYLVEQ LTKAHVNDVN FTP FKYQLS PSLPVKKDGP GKAIIVILSA LIGGMVACGG VLLRYAMASR KQDAMMADHL VEFRVPGSHH HHHHHH

UniProtKB: Ferric enterobactin transport protein FepE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.0 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Details: 40 seconds at 20 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 15386 / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 918682
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 210303
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.7)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.7)
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. 4.7)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 142
Output model

PDB-9ski:
Polysaccharide co-polymerase FepE open 7 subunit complex

+
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