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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Acinetobacter GP16 Type IV pilus | |||||||||
![]() | map | |||||||||
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![]() | T4P / Competence / CELL ADHESION | |||||||||
Function / homology | ![]() protein secretion by the type II secretion system / type II protein secretion system complex / pilus / cell adhesion / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.14 Å | |||||||||
![]() | Meng R / Xing Z / Zhang J | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 122.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.5 KB 17.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.6 KB | Display | ![]() |
Images | ![]() | 51.1 KB | ||
Filedesc metadata | ![]() | 5.5 KB | ||
Others | ![]() ![]() | 226.3 MB 226.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8tobMC ![]() 8tocC ![]() 8tv9C ![]() 8tvaC ![]() 8tw2C ![]() 8twcC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: A
File | emd_41442_half_map_1.map | ||||||||||||
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Annotation | A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: B
File | emd_41442_half_map_2.map | ||||||||||||
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Annotation | B | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Acinetobacter genomosp.16 Tyoe IV pilus
Entire | Name: Acinetobacter genomosp.16 Tyoe IV pilus |
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Components |
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-Supramolecule #1: Acinetobacter genomosp.16 Tyoe IV pilus
Supramolecule | Name: Acinetobacter genomosp.16 Tyoe IV pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Filamentous Type IV pilus |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11 kDa/nm |
-Macromolecule #1: Fimbrial protein
Macromolecule | Name: Fimbrial protein / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 7.470747 KDa |
Sequence | String: TLIELMIVVA IIGILAAIAI PQYQNYIAKS QVSRVMSETG SLKTVIETCI LDGKTAANCE LGWTNSNLLG UniProtKB: Fimbrial protein |
-Macromolecule #2: Fimbrial protein
Macromolecule | Name: Fimbrial protein / type: protein_or_peptide / ID: 2 / Number of copies: 22 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 6.999778 KDa |
Sequence | String: STAAVTGQTG LTITYPASAT ESAAIQGTFG NSAAIKIKNQ TLTWTRTPEG AWSCATTVEA KFKPAGCAS UniProtKB: Fimbrial protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Concentration | 1.35 mg/mL | |||||||||
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Buffer | pH: 8 Component:
Details: 20mM Tris-HCl, 200mM NaCl, pH 8.0 | |||||||||
Grid | Model: 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. | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III / Details: 3uL sample applied to a QuantiFoil R2/1 grid. | |||||||||
Details | vitreous Typy IV pilus |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: BACKBONE TRACE |
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Output model | ![]() PDB-8tob: |