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- EMDB-41442: Acinetobacter GP16 Type IV pilus -

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Basic information

Entry
Database: EMDB / ID: EMD-41442
TitleAcinetobacter GP16 Type IV pilus
Map datamap
Sample
  • Complex: Acinetobacter genomosp.16 Tyoe IV pilus
    • Protein or peptide: Fimbrial protein
    • Protein or peptide: Fimbrial protein
KeywordsT4P / Competence / CELL ADHESION
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / pilus / cell adhesion / membrane
Similarity search - Function
Bacterial general secretion pathway protein G-type pilin / 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
Biological speciesAcinetobacter genomosp. 16BJ (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsMeng R / Xing Z / Zhang J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01GM141659 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis of Acinetobacter type IV pili targeting by an RNA virus.
Authors: Ran Meng / Zhongliang Xing / Jeng-Yih Chang / Zihao Yu / Jirapat Thongchol / Wen Xiao / Yuhang Wang / Karthik Chamakura / Zhiqi Zeng / Fengbin Wang / Ry Young / Lanying Zeng / Junjie Zhang /
Abstract: Acinetobacters pose a significant threat to human health, especially those with weakened immune systems. Type IV pili of acinetobacters play crucial roles in virulence and antibiotic resistance. ...Acinetobacters pose a significant threat to human health, especially those with weakened immune systems. Type IV pili of acinetobacters play crucial roles in virulence and antibiotic resistance. Single-stranded RNA bacteriophages target the bacterial retractile pili, including type IV. Our study delves into the interaction between Acinetobacter phage AP205 and type IV pili. Using cryo-electron microscopy, we solve structures of the AP205 virion with an asymmetric dimer of maturation proteins, the native Acinetobacter type IV pili bearing a distinct post-translational pilin cleavage, and the pili-bound AP205 showing its maturation proteins adapted to pilin modifications, allowing each phage to bind to one or two pili. Leveraging these results, we develop a 20-kilodalton AP205-derived protein scaffold targeting type IV pili in situ, with potential for research and diagnostics.
History
DepositionAug 3, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41442.png

Downloads & links

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Map

FileDownload / File: emd_41442.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332.8 Å		0.83 Å/pix.
x 400 pix.
= 332.8 Å		0.83 Å/pix.
x 400 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.08914391 - 0.28763655
Average (Standard dev.)0.00016636743 (±0.010421797)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: A

Fileemd_41442_half_map_1.map
AnnotationA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: B

Fileemd_41442_half_map_2.map
AnnotationB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Acinetobacter genomosp.16 Tyoe IV pilus

EntireName: Acinetobacter genomosp.16 Tyoe IV pilus
Components
  • Complex: Acinetobacter genomosp.16 Tyoe IV pilus
    • Protein or peptide: Fimbrial protein
    • Protein or peptide: Fimbrial protein

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Supramolecule #1: Acinetobacter genomosp.16 Tyoe IV pilus

SupramoleculeName: Acinetobacter genomosp.16 Tyoe IV pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Filamentous Type IV pilus
Source (natural)Organism: Acinetobacter genomosp. 16BJ (bacteria)
Molecular weightTheoretical: 11 kDa/nm

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Macromolecule #1: Fimbrial protein

MacromoleculeName: Fimbrial protein / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter genomosp. 16BJ (bacteria)
Molecular weightTheoretical: 7.470747 KDa
SequenceString:
TLIELMIVVA IIGILAAIAI PQYQNYIAKS QVSRVMSETG SLKTVIETCI LDGKTAANCE LGWTNSNLLG

UniProtKB: Fimbrial protein

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Macromolecule #2: Fimbrial protein

MacromoleculeName: Fimbrial protein / type: protein_or_peptide / ID: 2 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter genomosp. 16BJ (bacteria)
Molecular weightTheoretical: 6.999778 KDa
SequenceString:
STAAVTGQTG LTITYPASAT ESAAIQGTFG NSAAIKIKNQ TLTWTRTPEG AWSCATTVEA KFKPAGCAS

UniProtKB: Fimbrial protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1.35 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris (hydroxymethyl) aminomethane (THAM) hydrochloride
200.0 mMNaClSodium Chloride

Details: 20mM Tris-HCl, 200mM NaCl, pH 8.0
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 100 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III / Details: 3uL sample applied to a QuantiFoil R2/1 grid.
Detailsvitreous Typy IV pilus

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 135000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 10.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 92 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 900000
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: BACKBONE TRACE
Output model

PDB-8tob:
Acinetobacter GP16 Type IV pilus

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