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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 datafinal map
Sample
  • Complex: FljK + FljL filament
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Flagellin / Flagellin FljK
Similarity search - Component
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.
History
DepositionJun 27, 2020-
Header (metadata) releaseDec 23, 2020-
Map releaseDec 23, 2020-
UpdateAug 18, 2021-
Current statusAug 18, 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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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22232.png

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)
Annotationfinal map
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

Histogram

Histogram (log scale)
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/NZ500500500
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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Mask #1

Fileemd_22232_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_22232_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FljK + FljL filament

EntireName: FljK + FljL filament
Components
  • Complex: FljK + FljL filament

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Supramolecule #1: FljK + FljL filament

SupramoleculeName: FljK + FljL filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Caulobacter vibrioides NA1000 (bacteria)

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.88 Å
Applied symmetry - Helical parameters - Δ&Phi: 65.6 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 54743
CTF correctionSoftware - Name: RELION (ver. 3.1)
Startup modelType of model: OTHER / Details: featureless cylinder
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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