+Open data
-Basic information
Entry | Database: PDB / ID: 8tob | ||||||
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Title | Acinetobacter GP16 Type IV pilus | ||||||
Components | (Fimbrial protein) x 2 | ||||||
Keywords | CELL ADHESION / T4P / Competence | ||||||
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 | ||||||
Biological species | Acinetobacter genomosp. 16BJ (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.14 Å | ||||||
Authors | Meng, R. / Xing, Z. / Zhang, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tob.cif.gz | 472 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tob.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8tob.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tob_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8tob_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8tob_validation.xml.gz | 80 KB | Display | |
Data in CIF | 8tob_validation.cif.gz | 125.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/8tob ftp://data.pdbj.org/pub/pdb/validation_reports/to/8tob | HTTPS FTP |
-Related structure data
Related structure data | 41442MC 8tocC 8tv9C 8tvaC 8tw2C 8twcC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 7470.747 Da / Num. of mol.: 22 / Fragment: residues 9-78 / Source method: isolated from a natural source / Source: (natural) Acinetobacter genomosp. 16BJ (bacteria) / References: UniProt: N9RQW9 #2: Protein | Mass: 6999.778 Da / Num. of mol.: 22 / Fragment: residues 79-147 / Source method: isolated from a natural source / Source: (natural) Acinetobacter genomosp. 16BJ (bacteria) / References: UniProt: N9RQW9 Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Acinetobacter genomosp.16 Tyoe IV pilus / Type: COMPLEX / Details: Filamentous Type IV pilus / Entity ID: all / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 11 kDa/nm / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Acinetobacter genomosp. 16BJ (bacteria) | |||||||||||||||
Buffer solution | pH: 8 / Details: 20mM Tris-HCl, 200mM NaCl, pH 8.0 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 1.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: vitreous Typy IV pilus | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3uL sample applied to a QuantiFoil R2/1 grid |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 135000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 200 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.19.2_4158: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 92 ° / Axial rise/subunit: 10 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 900000 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE | ||||||||||||||||||||||||
Refine LS restraints |
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