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- EMDB-42136: PhiCb5 maturation protein with Caulobacter crescentus bNY30a pili -

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Basic information

Entry
Database: EMDB / ID: EMD-42136
TitlePhiCb5 maturation protein with Caulobacter crescentus bNY30a pili
Map dataCaulobacter pilus binds to phiCb5
Sample
  • Complex: A complex of pilus and phiCb5 maturation protein
    • Protein or peptide: Maturation protein
    • Protein or peptide: Flp family type IVb pilin
KeywordsRNA phage / protein fibril / RECOMBINATION
Function / homologyFlp/Fap pilin component / Flp/Fap pilin component / Assembly protein / Phage maturation protein / virion attachment to host cell pilus / membrane / Flp family type IVb pilin / Maturation protein
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria) / Caulobacter phage phiCb5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.45 Å
AuthorsWang Y / Zhang J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1R01GM141659 United States
CitationJournal: Sci Adv / Year: 2024
Title: Structural mechanisms of Tad pilus assembly and its interaction with an RNA virus.
Authors: Yuhang Wang / Matthew Theodore / Zhongliang Xing / Utkarsh Narsaria / Zihao Yu / Lanying Zeng / Junjie Zhang /
Abstract: Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV ... Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV pilins, Tad pilins lack the typical globular β sheet domain responsible for pilus assembly and phage binding. The mechanisms of Tad pilus assembly and its interaction with phage ΦCb5 have been elusive. Using cryo-electron microscopy, we unveiled the Tad pilus assembly mechanism, featuring a unique network of hydrogen bonds at its core. We then identified the Tad pilus binding to the ΦCb5 maturation protein (Mat) through its β region. Notably, the amino terminus of ΦCb5 Mat is exposed outside the capsid and phage/pilus interface, enabling the attachment of fluorescent and affinity tags. These engineered ΦCb5 virions can be efficiently assembled and purified in , maintaining infectivity against , which presents promising applications, including RNA delivery and phage display.
History
DepositionSep 27, 2023-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42136.png

Downloads & links

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Map

FileDownload / File: emd_42136.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCaulobacter pilus binds to phiCb5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 600 pix.
= 516. Å		0.86 Å/pix.
x 600 pix.
= 516. Å		0.86 Å/pix.
x 600 pix.
= 516. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00127
Minimum - Maximum-0.009021176 - 0.029680962
Average (Standard dev.)-0.000104819 (±0.0018826334)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 516.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Caulobacter pilus binds to phiCb5

Fileemd_42136_half_map_1.map
AnnotationCaulobacter pilus binds to phiCb5
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Caulobacter pilus binds to phiCb5

Fileemd_42136_half_map_2.map
AnnotationCaulobacter pilus binds to phiCb5
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A complex of pilus and phiCb5 maturation protein

EntireName: A complex of pilus and phiCb5 maturation protein
Components
  • Complex: A complex of pilus and phiCb5 maturation protein
    • Protein or peptide: Maturation protein
    • Protein or peptide: Flp family type IVb pilin

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Supramolecule #1: A complex of pilus and phiCb5 maturation protein

SupramoleculeName: A complex of pilus and phiCb5 maturation protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: A complex of Caulobacter crescentus pilus and ssRNA phage phiCb5 maturation protein in buffer
Source (natural)Organism: Caulobacter vibrioides (bacteria)
Molecular weightTheoretical: 210 KDa

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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: Caulobacter phage phiCb5 (virus)
Molecular weightTheoretical: 40.725336 KDa
SequenceString: MARIRNRSSI ASSGMSTFYL FGTPIVNEEI IVRNTEWCSD VIGNPGDNPL DIHKQEWTIK PLSGQIIFGS GTYRSLQCPP EYCRGASLS HLSLPSQSGL GTTALARTNP SRPAFNLPAF IGELRDLPRM FKIAGDTMLR KGANAFLSYQ FGWKPLISDI S KALDFSAT ...String:
MARIRNRSSI ASSGMSTFYL FGTPIVNEEI IVRNTEWCSD VIGNPGDNPL DIHKQEWTIK PLSGQIIFGS GTYRSLQCPP EYCRGASLS HLSLPSQSGL GTTALARTNP SRPAFNLPAF IGELRDLPRM FKIAGDTMLR KGANAFLSYQ FGWKPLISDI S KALDFSAT VRTRSDEWHR LYSNGGLKRR INLGVDIEQK KENDVVLHSS NGFVVASHTV ITVRKTWATV RWRPDAGSLP PI TKSSSEK HARALLGLGV GGLIEGAWQL MPWSWMVDWF GNVGTFLQAS NNTIGASPGL VNIMTTTTTN HQFSVKRDLS DGW IKGGDC SATVTSKARS QSSGPTITAS IPNLSGRQLS ILGALGIQRV PRHLLR

UniProtKB: Maturation protein

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Macromolecule #2: Flp family type IVb pilin

MacromoleculeName: Flp family type IVb pilin / type: protein_or_peptide / ID: 2 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Caulobacter vibrioides (bacteria)
Molecular weightTheoretical: 4.37914 KDa
SequenceString:
ATAIEYGLIV ALIAVVIVTA VTTLGTKLNL AFTKAGTAVS TAAGT

UniProtKB: Flp family type IVb pilin

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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: 7.5
Component:
ConcentrationFormulaName
2.0 mMMgCl2Magnesium chloride
20.0 mMC4H11NO3Tris

Details: 20mM tris, 2mM MgCl2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 25.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56330
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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