+Open data
-Basic information
Entry | Database: PDB / ID: 8toc | ||||||
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Title | Acinetobacter phage AP205 | ||||||
Components |
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Keywords | VIRUS/RNA / Acinetobacter / SsRNA phage virus / VIRUS / VIRUS-RNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteria abnormis (insect) Acinetobacter phage AP205 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å | ||||||
Authors | Meng, R. / Xing, Z. / Chang, J. / 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 | 8toc.cif.gz | 5.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8toc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8toc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8toc_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8toc_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8toc_validation.xml.gz | 502 KB | Display | |
Data in CIF | 8toc_validation.cif.gz | 917 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/8toc ftp://data.pdbj.org/pub/pdb/validation_reports/to/8toc | HTTPS FTP |
-Related structure data
Related structure data | 41443MC 8tobC 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: RNA chain | Mass: 1368509.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: genomic RNA / Source: (natural) Bacteria abnormis (insect) | ||
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#2: Protein | Mass: 61063.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acinetobacter phage AP205 (virus) / References: UniProt: Q9AZ43 #3: Protein | Mass: 13820.569 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Source: (natural) Acinetobacter phage AP205 (virus) / References: UniProt: Q9AZ42 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Acinetobacter phage AP205 / Type: VIRUS Details: amplified and purified from infected Acinetobacter GP16 cells. Entity ID: #1, #3, #2 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 3.94 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Acinetobacter phage AP205 (virus) | |||||||||||||||
Details of virus | Empty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION | |||||||||||||||
Natural host | Organism: Acinetobacter genomosp. 16BJ | |||||||||||||||
Virus shell | Name: Coat / 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 | |||||||||||||||
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 300-mesh 2/1 copper 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: 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) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150000 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Refine LS restraints |
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