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- EMDB-41635: Outer Mat-T4P complex -

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Basic information

Entry
Database: EMDB / ID: EMD-41635
TitleOuter Mat-T4P complex
Map data
Sample
  • Virus: Acinetobacter phage AP205 (virus)
    • Protein or peptide: Maturation protein
    • Protein or peptide: Fimbrial protein
    • Protein or peptide: Fimbrial protein
KeywordsAcinetobacter / SsRNA phage virus / T4P / VIRUS
Function / homology
Function and homology information


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
Assembly protein / Phage maturation protein / Bacterial general secretion pathway protein G-type pilin / Fimbrial protein pilin / Pilin (bacterial filament) / : / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Fimbrial protein / Maturation protein
Similarity search - Component
Biological speciesAcinetobacter phage AP205 (virus) / Acinetobacter genomosp. 16BJ (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.55 Å
AuthorsMeng R / Xing Z / Thongchol J / 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 17, 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_41635.png

Downloads & links

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Map

FileDownload / File: emd_41635.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.12 Å/pix.
x 350 pix.
= 742. Å		2.12 Å/pix.
x 350 pix.
= 742. Å		2.12 Å/pix.
x 350 pix.
= 742. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.29
Minimum - Maximum-2.519237 - 5.52014
Average (Standard dev.)-0.0028496215 (±0.13593338)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 741.99994 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41635_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41635_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: Maturation protein
    • Protein or peptide: Fimbrial protein
    • Protein or peptide: Fimbrial protein

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Supramolecule #1: Acinetobacter phage AP205

SupramoleculeName: Acinetobacter phage AP205 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / 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: 378 KDa
Virus shellShell ID: 1 / Name: Coat Capsid / Diameter: 290.0 Å / T number (triangulation number): 3

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Macromolecule #1: Maturation protein

MacromoleculeName: Maturation protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter phage AP205 (virus)
Molecular weightTheoretical: 61.063852 KDa
SequenceString: MNMYKWVPES IRDSGEGQPS YSNNGDYAPS GPWVAAGIHT MPQSLRDSMR NSIMVTAQAR RDVIGPEWGP DGRFTGYASV IGTPDPKPA DIVNKFTVER RPVSNGNFQQ RVKAGDIVVA PYTSDGKITV KLVAGQKDIS STPDYDYRID SSLASSAGFV V AGERWYYT ...String:
MNMYKWVPES IRDSGEGQPS YSNNGDYAPS GPWVAAGIHT MPQSLRDSMR NSIMVTAQAR RDVIGPEWGP DGRFTGYASV IGTPDPKPA DIVNKFTVER RPVSNGNFQQ RVKAGDIVVA PYTSDGKITV KLVAGQKDIS STPDYDYRID SSLASSAGFV V AGERWYYT KRHFIIPRYF QNWRMRRRKY VTGWVMPTFY SPKEIFNRLK DSLVPDTGLV TQVWADNNTK RMDFLTAMAE IP QTLSSFL DALGYLGSLI KDFKRRRFFL NKAHQRIRNK LGVSFAERRS QIVSKYDRKI ASARKPAIIV KLRQRKEKAL KAL DKMRVR EEKKMIREFA TQAASLWLSF RYEIMPLYYQ SQDVLDVIAN STSEFMTSRD FVAKAINIGI PLEWNLDQEN LVSQ PRHNV MVKSKLSPEN NIGKTLSVNP FTTAWELLTL SFVVDWFVNF GDVIAGFTGG YSDDSGATAS WRFDDKKVFH LKNIP SAMV IVDINFYTRQ VIDPRLCGGL AFSPKLNLFR YLDAMSLSWN RSRLKISRAT

UniProtKB: Maturation protein

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Macromolecule #2: Fimbrial protein

MacromoleculeName: Fimbrial protein / type: protein_or_peptide / ID: 2 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter genomosp. 16BJ (bacteria)
Molecular weightTheoretical: 7.470747 KDa
SequenceString:
TLIELMIVVA IIGILAAIAI PQYQNYIAKS QVSRVMSETG SLKTVIETCI LDGKTAANCE LGWTNSNLLG

UniProtKB: Fimbrial protein

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Macromolecule #3: Fimbrial protein

MacromoleculeName: Fimbrial protein / type: protein_or_peptide / ID: 3 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter genomosp. 16BJ (bacteria)
Molecular weightTheoretical: 6.999778 KDa
SequenceString:
STAAVTGQTG LTITYPASAT ESAAIQGTFG NSAAIKIKNQ TLTWTRTPEG AWSCATTVEA KFKPAGCAS

UniProtKB: Fimbrial 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: 8.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 16000
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-8tva:
Outer Mat-T4P complex

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