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- EMDB-41625: Type IV pilus from Pseudomonas PAO1 strain -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-41625
TitleType IV pilus from Pseudomonas PAO1 strainPilus
Map dataType IV pilus from Pseudomonas PAO1 strainPilus
Sample
  • Organelle or cellular component: Type IV twitching pilus
    • Protein or peptide: Type IV major pilin protein PilA
KeywordsType IV pilus / T4P / PAO1 / MEMBRANE PROTEIN
Function / homology
Function and homology information


type IV pilus / type IV pilus-dependent motility / single-species biofilm formation on inanimate substrate / cell adhesion involved in single-species biofilm formation / pilus / regulation of calcium-mediated signaling / host cell endoplasmic reticulum membrane / cell surface / plasma membrane / cytosol
Similarity search - Function
Fimbrial protein pilin / Pilin (bacterial filament) / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Type IV major pilin protein PilA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria) / Pseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsThongchol J / Zhang J / Zeng L
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI156846 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141659 United States
National Science Foundation (NSF, United States)MCB-1902392 United States
Other privateTexas A&M University T3
Other privateTexas A&M University X-grants
Other privateCenter for phage technology, TAMU
Other privateCenter for the Physics of Biological Functions PHY-1734030
CitationJournal: Science / Year: 2024
Title: Removal of type IV pili by a small RNA virus.
Authors: Jirapat Thongchol / Zihao Yu / Laith Harb / Yiruo Lin / Matthias Koch / Matthew Theodore / Utkarsh Narsaria / Joshua Shaevitz / Zemer Gitai / Yinghao Wu / Junjie Zhang / Lanying Zeng /
Abstract: The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen . The single-stranded RNA (ssRNA) phage PP7 binds to T4P and is brought to the cell surface through ...The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen . The single-stranded RNA (ssRNA) phage PP7 binds to T4P and is brought to the cell surface through pilus retraction. Using fluorescence microscopy, we discovered that PP7 detaches T4P, which impairs cell motility and restricts the pathogen's virulence. Using cryo-electron microscopy, mutagenesis, optical trapping, and Langevin dynamics simulation, we resolved the structure of PP7, T4P, and the PP7/T4P complex and showed that T4P detachment is driven by the affinity between the phage maturation protein and its bound pilin, plus the pilus retraction force and speed, and pilus bending. Pilus detachment may be widespread among other ssRNA phages and their retractile pilus systems and offers new prospects for antibacterial prophylaxis and therapeutics.
History
DepositionAug 16, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41625.png

Downloads & links

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Map

FileDownload / File: emd_41625.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationType IV pilus from Pseudomonas PAO1 strain
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.35671583 - 0.8156863
Average (Standard dev.)-0.0068778316 (±0.042004656)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 309.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Type IV twitching pilus

EntireName: Type IV twitching pilus
Components
  • Organelle or cellular component: Type IV twitching pilus
    • Protein or peptide: Type IV major pilin protein PilA

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Supramolecule #1: Type IV twitching pilus

SupramoleculeName: Type IV twitching pilus / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1
Molecular weightTheoretical: 240 KDa

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Macromolecule #1: Type IV major pilin protein PilA

MacromoleculeName: Type IV major pilin protein PilA / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1
Molecular weightTheoretical: 14.878889 KDa
SequenceString:
FTLIELMIVV AIIGILAAIA IPQYQNYVAR SEGASALATI NPLKTTVEES LSRGIAGSKI KIGTTASTAT ETYVGVEPDA NKLGVIAVA IEDSGAGDIT FTFQTGTSSP KNATKVITLN RTADGVWACK STQDPMFTPK GCDN

UniProtKB: Type IV major pilin protein PilA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4 / Component - Concentration: 1.0 x / Component - Name: PBS
Details: 137 mM NaCl, 2.7 mM KCl, 8 mM Na2HPO4, and 2 mM KH2PO4, pH 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 5085 / Average electron dose: 50.85 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 25763
Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14424
FSC plot (resolution estimation)

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