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- PDB-9h80: Structure of the outer membrane exopolysaccharide transporter PelBC -

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Basic information

Entry
Database: PDB / ID: 9h80
TitleStructure of the outer membrane exopolysaccharide transporter PelBC
Components
  • PelB
  • PelC
KeywordsTRANSPORT PROTEIN / Exopolysaccharide / Complex / Acyl-chain
Function / homology
Function and homology information


polysaccharide transport / polysaccharide biosynthetic process / single-species biofilm formation / membrane
Similarity search - Function
PelB, C-terminal beta barrel domain / Tetratricopeptide repeat / : / Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
PHOSPHATIDYLETHANOLAMINE / PelB / PelC
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsBenedens, M. / Rosales, C. / Beckmann, R. / Kedrov, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2025
Title: Assembly and the gating mechanism of the Pel exopolysaccharide export complex PelBC of Pseudomonas aeruginosa.
Authors: Marius Benedens / Cristian Rosales-Hernandez / Sabine A P Straathof / Jennifer Loschwitz / Otto Berninghausen / Giovanni Maglia / Roland Beckmann / Alexej Kedrov /
Abstract: The pathogen Pseudomonas aeruginosa enhances its virulence and antibiotic resistance upon formation of durable biofilms. The exopolysaccharides Pel, Psl and alginate essentially contribute to the ...The pathogen Pseudomonas aeruginosa enhances its virulence and antibiotic resistance upon formation of durable biofilms. The exopolysaccharides Pel, Psl and alginate essentially contribute to the biofilm matrix, but their secretion mechanisms are barely understood. Here, we reveal the architecture of the outer membrane complex PelBC for Pel export, where the essential periplasmic ring of twelve lipoproteins PelC is mounted on top of the nanodisc-embedded β-barrel PelB. The PelC assembly is stabilized by electrostatic contacts with the periplasmic rim of PelB and via the membrane-anchored acyl chains. The negatively charged interior of the PelB β-barrel forms a route for the cationic Pel exopolysaccharide. The β-barrel is sealed at the extracellular side, but molecular dynamic simulations suggest that the short loop Plug-S is sufficiently flexible to open a tunnel for the exopolysaccharide transport. This gating model is corroborated by single-channel conductivity measurements, where a deletion of Plug-S renders a constitutively open β-barrel. Our structural and functional analysis offers a comprehensive view on this pathogenicity-relevant complex and suggests the route taken by the exopolysaccharide at the final secretion step.
History
DepositionOct 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: PelB
C: PelC
D: PelC
E: PelC
F: PelC
G: PelC
H: PelC
I: PelC
J: PelC
K: PelC
L: PelC
A: PelC
B: PelC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)379,41040
Polymers359,59113
Non-polymers19,81927
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein PelB


Mass: 135273.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pelB, PA3063 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HZE5
#2: Protein
PelC


Mass: 18693.111 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pelC, PA3062 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HZE6
#3: Chemical...
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Exopolysaccharide transporter PelBC / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123975 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00318040
ELECTRON MICROSCOPYf_angle_d0.65324366
ELECTRON MICROSCOPYf_dihedral_angle_d8.9012717
ELECTRON MICROSCOPYf_chiral_restr0.0392586
ELECTRON MICROSCOPYf_plane_restr0.0063232

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