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- EMDB-41632: Asymmetric reconstruction of mature PP7 virions -

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Basic information

Entry
Database: EMDB / ID: EMD-41632
TitleAsymmetric reconstruction of mature PP7 virions
Map dataThe mature PP7 virion
Sample
  • Organelle or cellular component: Type IV twitching pilus
KeywordsssRNA phage / PP7 / Pepevirus / VIRUS
Function / homology
Function and homology information


virion attachment to host cell pilus / T=3 icosahedral viral capsid / virion component / regulation of translation / symbiont entry into host cell / RNA binding / identical protein binding
Similarity search - Function
Bacteriophage PP7, coat / Phage PP7 coat protein / Assembly protein / Phage maturation protein / Bacteriophage RNA-type, capsid
Similarity search - Domain/homology
Capsid protein / Maturation protein A
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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 17, 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_41632.png

Downloads & links

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Map

FileDownload / File: emd_41632.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe mature PP7 virion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 480 pix.
= 412.8 Å		0.86 Å/pix.
x 480 pix.
= 412.8 Å		0.86 Å/pix.
x 480 pix.
= 412.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.0054724603 - 0.031188482
Average (Standard dev.)0.00074899476 (±0.003360358)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 412.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_41632_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_41632_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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

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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: #1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1
Molecular weightTheoretical: 240 KDa

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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

Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 644601

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