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- EMDB-41666: Acinetobacter phage AP205 T=3 VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-41666
TitleAcinetobacter phage AP205 T=3 VLP
Map data
Sample
  • Virus: Acinetobacter phage AP205 (virus)
    • Protein or peptide: Coat protein
KeywordsAcinetobacter / SsRNA phage virus / VIRUS / VLP / VIRUS LIKE PARTICLE
Function / homology: / AP205 coat protein / viral capsid / Coat protein
Function and homology information
Biological speciesAcinetobacter phage AP205 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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 20, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41666.png

Downloads & links

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Map

FileDownload / File: emd_41666.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 432 pix.
= 457.92 Å		1.06 Å/pix.
x 432 pix.
= 457.92 Å		1.06 Å/pix.
x 432 pix.
= 457.92 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.0015788277 - 1.9093446
Average (Standard dev.)0.0056861043 (±0.055255927)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 457.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41666_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41666_half_map_2.map
Projections & Slices
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Sample components

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Entire : Acinetobacter phage AP205

EntireName: Acinetobacter phage AP205 (virus)
Components
  • Virus: Acinetobacter phage AP205 (virus)
    • Protein or peptide: Coat protein

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Supramolecule #1: Acinetobacter phage AP205

SupramoleculeName: Acinetobacter phage AP205 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: amplified and purified from infected Acinetobacter GP16 cells.
NCBI-ID: 154784 / Sci species name: Acinetobacter phage AP205 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Acinetobacter genomosp. 16BJ (bacteria)
Molecular weightTheoretical: 2.48 MDa
Virus shellShell ID: 1 / Name: Coat / Diameter: 300.0 Å / T number (triangulation number): 3

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Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 180 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter phage AP205 (virus)
Molecular weightTheoretical: 13.820569 KDa
SequenceString:
ANKPMQPITS TANKIVWSDP TRLSTTFSAS LLRQRVKVGI AELNNVSGQY VSVYKRPAPK PEGCADACVI MPNENQSIRT VISGSAENL ATLKAEWETH KRNVDTLFAS GNAGLGFLDP TAAIVSSDTT

UniProtKB: Coat protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris (hydroxymethyl) aminomethane (THAM) hydrochloride
150.0 mMNaClsodium chloride

Details: 20mM Tris-HCl, 150mM NaCl, pH 8.0
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III / Details: 3uL sample applied to a 300-mesh 2/1 copper grid.
DetailsAP205 virion particle

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / 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: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 10000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8twc:
Acinetobacter phage AP205 T=3 VLP

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