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- EMDB-22232: Caulobacter crescentus FljK + FljL filament -

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Basic information

Entry
Database: EMDB / ID: EMD-22232
TitleCaulobacter crescentus FljK + FljL filament
Map data
SampleFljK + FljL filament
Biological speciesCaulobacter vibrioides NA1000 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsMontemayor EJ / Ploscariu NT / Sanchez JC / Parrell D / Dillard RS / Shebelut CW / Ke Z / Guerrero-Ferreira RC / Wright ER
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104540 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104540-03S1 United States
National Science Foundation (NSF, United States)0923395 United States
National Institutes of Health/Office of the DirectorS10 OD018142-01 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR025080-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM116788 United States
CitationJournal: J Bacteriol / Year: 2021
Title: Flagellar Structures from the Bacterium Caulobacter crescentus and Implications for Phage CbK Predation of Multiflagellin Bacteria.
Authors: Eric J Montemayor / Nicoleta T Ploscariu / Juan C Sanchez / Daniel Parrell / Rebecca S Dillard / Conrad W Shebelut / Zunlong Ke / Ricardo C Guerrero-Ferreira / Elizabeth R Wright /
Abstract: is a Gram-negative alphaproteobacterium that commonly lives in oligotrophic fresh- and saltwater environments. is a host to many bacteriophages, including ϕCbK and ϕCbK-like bacteriophages, which ... is a Gram-negative alphaproteobacterium that commonly lives in oligotrophic fresh- and saltwater environments. is a host to many bacteriophages, including ϕCbK and ϕCbK-like bacteriophages, which require interaction with the bacterial flagellum and pilus complexes during adsorption. It is commonly thought that the six paralogs of the flagellin gene present in are important for bacteriophage evasion. Here, we show that deletion of specific flagellins in can indeed attenuate ϕCbK adsorption efficiency, although no single deletion completely ablates ϕCbK adsorption. Thus, the bacteriophage ϕCbK likely recognizes a common motif among the six known flagellins in with various degrees of efficiency. Interestingly, we observe that most deletion strains still generate flagellar filaments, with the exception of a strain that contains only the most divergent flagellin, FljJ, or a strain that contains only FljN and FljO. To visualize the surface residues that are likely recognized by ϕCbK, we determined two high-resolution structures of the FljK filament, with and without an amino acid substitution that induces straightening of the filament. We observe posttranslational modifications on conserved surface threonine residues of FljK that are likely O-linked glycans. The possibility of interplay between these modifications and ϕCbK adsorption is discussed. We also determined the structure of a filament composed of a heterogeneous mixture of FljK and FljL, the final resolution of which was limited to approximately 4.6 Å. Altogether, this work builds a platform for future investigations of how phage ϕCbK infects at the molecular level. Bacterial flagellar filaments serve as an initial attachment point for many bacteriophages to bacteria. Some bacteria harbor numerous flagellin genes and are therefore able to generate flagellar filaments with complex compositions, which is thought to be important for evasion from bacteriophages. This study characterizes the importance of the six flagellin genes in for infection by bacteriophage ϕCbK. We find that filaments containing the FljK flagellin are the preferred substrate for bacteriophage ϕCbK. We also present a high-resolution structure of a flagellar filament containing only the FljK flagellin, which provides a platform for future studies on determining how bacteriophage ϕCbK attaches to flagellar filaments at the molecular level.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJun 27, 2020-
Header (metadata) releaseDec 23, 2020-
Map releaseDec 23, 2020-
UpdateFeb 24, 2021-
Current statusFeb 24, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0212
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0212
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_22232.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.74 Å/pix.
x 160 pix.
= 278.4 Å
1.74 Å/pix.
x 160 pix.
= 278.4 Å
1.74 Å/pix.
x 160 pix.
= 278.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.74 Å
Density
Contour LevelBy AUTHOR: 0.0212 / Movie #1: 0.0212
Minimum - Maximum-0.029674092 - 0.07356479
Average (Standard dev.)-6.354064e-05 (±0.008208189)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 278.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.741.741.74
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z278.400278.400278.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ410410410
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0300.074-0.000

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Supplemental data

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Segmentation: #1

Fileemd_22232_msk_1.map
Projections & Slices
AxesZYX

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Half map: half map 1

Fileemd_22232_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: half map 2

Fileemd_22232_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Sample components

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Entire FljK + FljL filament

EntireName: FljK + FljL filament / Number of components: 1

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Component #1: protein, FljK + FljL filament

ProteinName: FljK + FljL filament / Recombinant expression: No
SourceSpecies: Caulobacter vibrioides NA1000 (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 4.88 Å / Delta phi: 65.6 %deg;
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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