9X0X | pdb_00009x0x

Pseudomonas aeruginosa (PAO1) Outer membrane PilQ (Secretin) with SlkB in C14 symmetry


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9X0X

This is version 1.0 of the entry. See complete history

Literature

Secretin-interacting plug proteins prevent antibiotic influx during type IV pilus assembly in Pseudomonas aeruginosa.

Kwon, O.H.Lee, Y.Ryu, B.Sher, J.W.Park, S.Lauber, F.Kim, B.O.Yoo, Y.Cho, S.H.Choe, D.Cho, Y.H.Collet, J.F.Ohi, M.D.Bernhardt, T.G.Chung, J.M.Cho, H.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-026-73864-w
  • Primary Citation Related Structures: 
    9X0W, 9X0X, 9X0Y

  • PubMed 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 (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.


  • Organizational Affiliation
    • Department of Biological Sciences, College of Natural Sciences, Sungkyunkwan University, Suwon, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 1,257.16 kDa 
  • Atom Count: 41,454 
  • Modeled Residue Count: 5,390 
  • Deposited Residue Count: 11,592 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fimbrial assembly protein PilQ
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N
714Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: pilQPA5040
UniProt
Find proteins for P34750 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P34750 
Go to UniProtKB:  P34750
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34750
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Multidrug transporter114Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: PA0359
UniProt
Find proteins for Q9I6D5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I6D5 
Go to UniProtKB:  Q9I6D5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I6D5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PTY

Query on PTY



Download:Ideal Coordinates CCD File
CA [auth E]
DA [auth O]
EA [auth O]
FA [auth S]
GA [auth P]
CA [auth E],
DA [auth O],
EA [auth O],
FA [auth S],
GA [auth P],
HA [auth Q],
IA [auth R],
JA [auth T],
KA [auth U],
LA [auth V],
MA [auth W],
NA [auth X],
OA [auth Z],
PA [auth a]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487
RECONSTRUCTIONcryoSPARC4.5.1

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2022R1C1C1003352
National Research Foundation (NRF, Korea)Korea, Republic OfRS-2024-00440289
National Research Foundation (NRF, Korea)Korea, Republic OfRS-2025-00522505
National Research Foundation (NRF, Korea)Korea, Republic OfRS-2023-00228746
National Research Foundation (NRF, Korea)Korea, Republic OfRS-2022-NR067344

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-10
    Type: Initial release