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- EMDB-54967: Polysaccharide co-polymerase FepE open 9 subunit complex -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-54967
TitlePolysaccharide co-polymerase FepE open 9 subunit complex
Map dataPolysaccharide co-polymerase FepE 9 subunit complex from E. coli. Main map.
Sample
  • Complex: Open 9 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: 3.3 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

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Structure visualization

Supplemental images

emd_54967.png

Downloads & links

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Map

FileDownload / File: emd_54967.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPolysaccharide co-polymerase FepE 9 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: 0.05
Minimum - Maximum-0.1697275 - 0.38864717
Average (Standard dev.)0.000845667 (±0.010582906)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Additional map: Polysaccharide co-polymerase FepE 9 subunit complex from E....

Fileemd_54967_additional_1.map
AnnotationPolysaccharide co-polymerase FepE 9 subunit complex from E. coli. Sharpened map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Polysaccharide co-polymerase FepE 9 subunit complex from E....

Fileemd_54967_half_map_1.map
AnnotationPolysaccharide co-polymerase FepE 9 subunit complex from E. coli. Half map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Polysaccharide co-polymerase FepE 9 subunit complex from E....

Fileemd_54967_half_map_2.map
AnnotationPolysaccharide co-polymerase FepE 9 subunit complex from E. coli. Half map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Open 9 subunit bacterial polysaccharide co-polymerase complex

EntireName: Open 9 subunit bacterial polysaccharide co-polymerase complex
Components
  • Complex: Open 9 subunit bacterial polysaccharide co-polymerase complex
    • Protein or peptide: Ferric enterobactin transport protein FepE

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Supramolecule #1: Open 9 subunit bacterial polysaccharide co-polymerase complex

SupramoleculeName: Open 9 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

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Macromolecule #1: Ferric enterobactin transport protein FepE

MacromoleculeName: Ferric enterobactin transport protein FepE / type: protein_or_peptide / ID: 1 / Number of copies: 9 / 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

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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

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

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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

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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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 226507
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)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 197
Output model

PDB-9skk:
Polysaccharide co-polymerase FepE open 9 subunit complex

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