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- EMDB-41844: Cryo-EM structure of C.crescentus bNY30a pilus complex -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-41844
TitleCryo-EM structure of C.crescentus bNY30a pilus complex
Map datamain
Sample
  • Complex: Caulobacter crescentus pili
    • Protein or peptide: Flp family type IVb pilin
KeywordsComplex / PROTEIN FIBRIL
Function / homologyFlp/Fap pilin component / Flp/Fap pilin component / membrane / Flp family type IVb pilin
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsWang Y / Zhang J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)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 5, 2023-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41844.png

Downloads & links

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Map

FileDownload / File: emd_41844.map.gz / Format: CCP4 / Size: 139.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 332 pix.
= 285.52 Å		0.86 Å/pix.
x 332 pix.
= 285.52 Å		0.86 Å/pix.
x 332 pix.
= 285.52 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: 0.24
Minimum - Maximum-0.223739 - 0.77155745
Average (Standard dev.)0.00031238547 (±0.027242662)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions332332332
Spacing332332332
CellA=B=C: 285.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: b

Fileemd_41844_half_map_1.map
Annotationb
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: a

Fileemd_41844_half_map_2.map
Annotationa
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Caulobacter crescentus pili

EntireName: Caulobacter crescentus pili
Components
  • Complex: Caulobacter crescentus pili
    • Protein or peptide: Flp family type IVb pilin

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Supramolecule #1: Caulobacter crescentus pili

SupramoleculeName: Caulobacter crescentus pili / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Caulobacter crescentus pili in buffer
Source (natural)Organism: Caulobacter vibrioides (bacteria)
Molecular weightTheoretical: 170 KDa

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Macromolecule #1: Flp family type IVb pilin

MacromoleculeName: Flp family type IVb pilin / type: protein_or_peptide / ID: 1 / Number of copies: 37 / 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
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
2.0 mMMgCl2Magnesium chloride
20.0 mMC4H11NO3Tris

Details: 20mM tris, 2mM MgCl2
GridModel: C-flat-2/1 / Material: COPPER
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

Final reconstructionApplied symmetry - Helical parameters - Δz: 14.69 Å
Applied symmetry - Helical parameters - Δ&Phi: 51.96 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 392496
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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