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- PDB-8tuw: Type IV pilus from Pseudomonas PAO1 strain with PP7 Maturation protein -

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Basic information

Entry
Database: PDB / ID: 8tuw
TitleType IV pilus from Pseudomonas PAO1 strain with PP7 Maturation protein
Components
  • Maturation protein A
  • Type IV major pilin protein PilA
KeywordsMEMBRANE PROTEIN / Type IV pilus / T4P / PAO1
Function / homology
Function and homology information


type IV pilus / type IV pilus-dependent motility / single-species biofilm formation on inanimate substrate / virion attachment to host cell pilus / cell adhesion involved in single-species biofilm formation / pilus / regulation of calcium-mediated signaling / virion component / host cell endoplasmic reticulum membrane / symbiont entry into host cell ...type IV pilus / type IV pilus-dependent motility / single-species biofilm formation on inanimate substrate / virion attachment to host cell pilus / cell adhesion involved in single-species biofilm formation / pilus / regulation of calcium-mediated signaling / virion component / host cell endoplasmic reticulum membrane / symbiont entry into host cell / cell surface / plasma membrane / cytosol
Similarity search - Function
Assembly protein / Phage maturation protein / 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 / Maturation protein A
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Pseudomonas phage PP7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsThongchol, J. / Zhang, J. / Zeng, L.
Funding support United States, 7items
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 United States
Other privateTexas A&M University X-grants United States
Other privateCenter for phage technology, TAMU United States
National Science Foundation (NSF, United States)PHY-1734030 United States
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 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
M1: Maturation protein A
a2: Type IV major pilin protein PilA
b2: Type IV major pilin protein PilA
c2: Type IV major pilin protein PilA
d2: Type IV major pilin protein PilA
e2: Type IV major pilin protein PilA
f2: Type IV major pilin protein PilA
g2: Type IV major pilin protein PilA
h2: Type IV major pilin protein PilA
i2: Type IV major pilin protein PilA
j2: Type IV major pilin protein PilA
k2: Type IV major pilin protein PilA
l2: Type IV major pilin protein PilA
m2: Type IV major pilin protein PilA
n2: Type IV major pilin protein PilA
o2: Type IV major pilin protein PilA
p2: Type IV major pilin protein PilA


Theoretical massNumber of molelcules
Total (without water)288,82617
Polymers288,82617
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Maturation protein A / MP / Assembly protein / A protein


Mass: 50763.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage PP7 (virus) / References: UniProt: Q38061
#2: Protein
Type IV major pilin protein PilA / Pilin


Mass: 14878.889 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pilA, fimA, PA4525 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: P04739

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Type IV twitching pilus / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.24 MDa / Experimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1
Buffer solutionpH: 7.4
Details: 137 mM NaCl, 2.7 mM KCl, 8 mM Na2HPO4, and 2 mM KH2PO4, pH 7.4
Buffer componentConc.: 1 x / Name: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 80 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50.85 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 5085

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Processing

EM softwareName: cryoSPARC / Category: 3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 25763
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40493 / Symmetry type: POINT

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