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- EMDB-66447: Pseudomonas aeruginosa (PAO1) Outer membrane PilQ (Secretin) in C... -

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Basic information

Entry
Database: EMDB / ID: EMD-66447
TitlePseudomonas aeruginosa (PAO1) Outer membrane PilQ (Secretin) in C14 symmetry
Map data
Sample
  • Complex: Pseudomonas aeruginosa (PAO1) Outer membrane PilQ (Secretin)
    • Protein or peptide: Fimbrial assembly protein PilQ
    • Protein or peptide: Multidrug transporter
  • Ligand: PHOSPHATIDYLETHANOLAMINE
Keywordstype IV pili / secretin / plug / outer membrane / permeability barrier / antibiotics / drug resistance / TRANSPORT PROTEIN
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
Fimbrial assembly protein PilQ / Multidrug transporter
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsKwon O / Lee Y / Ryu B / Yoo Y / Chung J / Cho H
Funding support Korea, Republic Of, 5 items
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, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66447.png

Downloads & links

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Map

FileDownload / File: emd_66447.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 480 pix.
= 388.8 Å		0.81 Å/pix.
x 480 pix.
= 388.8 Å		0.81 Å/pix.
x 480 pix.
= 388.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.49561068 - 0.91499573
Average (Standard dev.)0.0029408885 (±0.029881375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 388.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66447_msk_1.map
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Half map: #2

Fileemd_66447_half_map_1.map
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Half map: #1

Fileemd_66447_half_map_2.map
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Sample components

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Entire : Pseudomonas aeruginosa (PAO1) Outer membrane PilQ (Secretin)

EntireName: Pseudomonas aeruginosa (PAO1) Outer membrane PilQ (Secretin)
Components
  • Complex: Pseudomonas aeruginosa (PAO1) Outer membrane PilQ (Secretin)
    • Protein or peptide: Fimbrial assembly protein PilQ
    • Protein or peptide: Multidrug transporter
  • Ligand: PHOSPHATIDYLETHANOLAMINE

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Supramolecule #1: Pseudomonas aeruginosa (PAO1) Outer membrane PilQ (Secretin)

SupramoleculeName: Pseudomonas aeruginosa (PAO1) Outer membrane PilQ (Secretin)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)

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Macromolecule #1: Fimbrial assembly protein PilQ

MacromoleculeName: Fimbrial assembly protein PilQ / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 77.463703 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString: MNSGLSRLGI ALLAAMFAPA LLAADLEKLD VAALPGDRVE LKLQFDEPVA APRGYTIEQP ARIALDLPGV QNKLGTKNRE LSVGNTRSV TVVEAKDRTR LIINLTALSS YTTRVEGNNL FVVVGNSPAG ASVASAAPVK ASPAPASYAQ PIKPKPYVPA G RAIRNIDF ...String:
MNSGLSRLGI ALLAAMFAPA LLAADLEKLD VAALPGDRVE LKLQFDEPVA APRGYTIEQP ARIALDLPGV QNKLGTKNRE LSVGNTRSV TVVEAKDRTR LIINLTALSS YTTRVEGNNL FVVVGNSPAG ASVASAAPVK ASPAPASYAQ PIKPKPYVPA G RAIRNIDF QRGEKGEGNV VIDLSDPTLS PDIQEQGGKI RLDFAKTQLP DALRVRLDVK DFATPVQFVN ASAQSDRTSI TI EPSGLYD YLVYQTDNRL TVSIKPMTTE DAERRKKDNF AYTGEKLSLN FQDIDVRSVL QLIADFTDLN LVASDTVQGN ITL RLQNVP WDQALDLVLK TKGLDKRKLG NVLLVAPADE IAARERQELE AQKQIAELAP LRRELIQVNY AKAADIAKLF QSVT SDGGQ EGKEGGRGSI TVDDRTNSII AYQPQERLDE LRRIVSQLDI PVRQVMIEAR IVEANVGYDK SLGVRWGGAY HKGNW SGYG KDGNIGIKDE DGMNCGPIAG SCTFPTTGTS KSPSPFVDLG AKDATSGIGI GFITDNIILD LQLSAMEKTG NGEIVS QPK VVTSDKETAK ILKGSEVPYQ EASSSGATST SFKEAALSLE VTPQITPDNR IIVEVKVTKD APDYQNMLNG VPPINKN EV NAKILVNDGE TIVIGGVFSN EQSKSVEKVP FLGELPYLGR LFRRDTVTDR KNELLVFLTP RIMNNQAIAI GR

UniProtKB: Fimbrial assembly protein PilQ

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Macromolecule #2: Multidrug transporter

MacromoleculeName: Multidrug transporter / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 11.599263 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MNLFRTTALV LALTTGLSSM PALADAVQEN ASGDPMYTVE APPAYAMIGD LLIARPFLIA ATAVGAVAFV VSLPFTAASG SVGKAGQAL VVDPGKEAFV RCLGCTTSGY NHDES

UniProtKB: Multidrug transporter

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Macromolecule #3: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 3 / Number of copies: 14 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: ab initio model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 18241
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9x0w:
Pseudomonas aeruginosa (PAO1) Outer membrane PilQ (Secretin) in C14 symmetry

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