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- PDB-9x0y: Pseudomonas aeruginosa (PAO1) Outer membrane PilQ (Secretin) with... -

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Basic information

Entry
Database: PDB / ID: 9x0y
TitlePseudomonas aeruginosa (PAO1) Outer membrane PilQ (Secretin) with SlkA in C14 symmetry
Components
  • Fimbrial assembly protein PilQ
  • Multidrug transporter
KeywordsTRANSPORT PROTEIN / type IV pili / secretin / plug / outer membrane / permeability barrier / antibiotics / drug resistance
Function / homology
Function and homology information


type IV pilus assembly / protein secretion / cell outer membrane
Similarity search - Function
Type IV pilus secretin PilQ / : / AMIN domain / AMIN domain / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site ...Type IV pilus secretin PilQ / : / AMIN domain / AMIN domain / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain / Type II/III secretion system / Bacterial type II and III secretion system protein
Similarity search - Domain/homology
PHOSPHATIDYLETHANOLAMINE / Fimbrial assembly protein PilQ / Multidrug transporter
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsKwon, O. / Lee, Y. / Ryu, B. / Yoo, Y. / Chung, J. / Cho, H.
Funding support Korea, Republic Of, 5items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2022R1C1C1003352 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2024-00440289 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2025-00522505 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2023-00228746 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2022-NR067344 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2026
Title: Secretin-interacting plug proteins prevent antibiotic influx during type IV pilus assembly in Pseudomonas aeruginosa.
Authors: Oh Hyun Kwon / Yeseul Lee / Bumhan Ryu / Joel W Sher / Sohee Park / Frédéric Lauber / Bi-O Kim / Youngki Yoo / Seung-Hyun Cho / Donghui Choe / You-Hee Cho / Jean-François Collet / Melanie ...Authors: Oh Hyun Kwon / Yeseul Lee / Bumhan Ryu / Joel W Sher / Sohee Park / Frédéric Lauber / Bi-O Kim / Youngki Yoo / Seung-Hyun Cho / Donghui Choe / You-Hee Cho / Jean-François Collet / Melanie D Ohi / Thomas G Bernhardt / Jeong Min Chung / Hongbaek Cho /
Abstract: Type IV pili (T4P) are important virulence factors that mediate host attachment and other pathogenic functions. In Gram-negative bacteria, T4P are assembled from pilin subunits at the inner membrane ...Type IV pili (T4P) are important virulence factors that mediate host attachment and other pathogenic functions. In Gram-negative bacteria, T4P are assembled from pilin subunits at the inner membrane (IM) and extend through the outer membrane (OM) via secretin channels. Although essential for T4P function, secretin complexes can impair the OM permeability barrier, potentially allowing entry of toxic compounds. The mechanisms that prevent such influx remain poorly understood. Here, we identify SlkA and SlkB (PA5122 and PA5123) as periplasmic proteins that interact with the T4P secretin channel and block antibiotic influx. Our data indicate that these proteins function as physical plugs sealing the channel until the IM complex docks and pilus assembly begins. These findings demonstrate that Slk proteins and the IM complex function redundantly to maintain OM barrier integrity, and that their interaction with the secretin channel represents a promising target for antibiotic potentiation.
History
DepositionSep 30, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fimbrial assembly protein PilQ
O: Multidrug transporter
P: Multidrug transporter
Q: Multidrug transporter
R: Multidrug transporter
S: Multidrug transporter
T: Multidrug transporter
U: Multidrug transporter
V: Multidrug transporter
W: Multidrug transporter
X: Multidrug transporter
Y: Multidrug transporter
Z: Multidrug transporter
a: Multidrug transporter
b: Multidrug transporter
B: Fimbrial assembly protein PilQ
C: Fimbrial assembly protein PilQ
D: Fimbrial assembly protein PilQ
E: Fimbrial assembly protein PilQ
F: Fimbrial assembly protein PilQ
G: Fimbrial assembly protein PilQ
H: Fimbrial assembly protein PilQ
I: Fimbrial assembly protein PilQ
J: Fimbrial assembly protein PilQ
K: Fimbrial assembly protein PilQ
L: Fimbrial assembly protein PilQ
M: Fimbrial assembly protein PilQ
N: Fimbrial assembly protein PilQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,257,15842
Polymers1,246,88228
Non-polymers10,27714
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, C14 symmetry hetero-oligomer
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Fimbrial assembly protein PilQ


Mass: 77463.703 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pilQ, PA5040 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: P34750
#2: Protein
Multidrug transporter


Mass: 11599.263 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0359 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9I6D5
#3: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
Has ligand of interestN
Has protein modificationY

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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: Pseudomonas aeruginosa (PAO1) Outer membrane PilQ (Secretin) with SlkA
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Source (recombinant)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Buffer solutionpH: 8
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: 1800 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingElectron dose: 53.1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.1particle selection
2Topazparticle selection
5cryoSPARC4.5.1CTF correction
8UCSF ChimeraX1.10.1model fitting
10PHENIX1.20.1-4487model refinement
14cryoSPARC4.5.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63311 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: in silico model
RefinementCross valid method: NONE

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