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Open data
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Basic information
Entry | Database: PDB / ID: 8tva | ||||||
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Title | Outer Mat-T4P complex | ||||||
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![]() | VIRUS / Acinetobacter / SsRNA phage virus / T4P | ||||||
Function / homology | ![]() virion attachment to host cell pilus / protein secretion by the type II secretion system / type II protein secretion system complex / pilus / virion component / cell adhesion / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.55 Å | ||||||
![]() | Meng, R. / Xing, Z. / Thongchol, J. / 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 521.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 41635MC ![]() 8tobC ![]() 8tocC ![]() 8tv9C ![]() 8tw2C ![]() 8twcC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 61063.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
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#2: Protein | Mass: 7470.747 Da / Num. of mol.: 20 / Fragment: residues 9-78 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 6999.778 Da / Num. of mol.: 20 / Fragment: residues 79-147 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Acinetobacter phage AP205 / Type: VIRUS / Entity ID: all / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.378 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||
Details of virus | Empty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION | |||||||||||||||
Natural host | Organism: Acinetobacter genomosp. 16BJ | |||||||||||||||
Virus shell | Name: Coat Capsid / Diameter: 290 nm / Triangulation number (T number): 3 | |||||||||||||||
Buffer solution | pH: 8 / Details: 20mM Tris-HCl, 150mM NaCl, pH 8.0 | |||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: AP205 virion particle | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3uL sample applied to a 300-mesh 2/1 copper grid |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||
3D reconstruction | Resolution: 8.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16000 / Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT |