+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22229 | |||||||||||||||||||||
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Title | Caulobacter crescentus FljK filament, straightened | |||||||||||||||||||||
Map data | sharpened map, masked | |||||||||||||||||||||
Sample |
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Keywords | flagellum / flagellin / filament / helical / Caulobacter / motility / STRUCTURAL PROTEIN | |||||||||||||||||||||
Function / homology | Function and homology information bacterial-type flagellum / structural molecule activity / extracellular region Similarity search - Function | |||||||||||||||||||||
Biological species | Caulobacter vibrioides NA1000 (bacteria) / Caulobacter vibrioides (strain NA1000 / CB15N) (bacteria) | |||||||||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||||||||
Authors | Montemayor EJ / Ploscariu NT | |||||||||||||||||||||
Funding support | United States, 6 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22229.map.gz | 26.4 MB | EMDB map data format | |
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Header (meta data) | emd-22229-v30.xml emd-22229.xml | 17.8 KB 17.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22229_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_22229.png | 122.9 KB | ||
Masks | emd_22229_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-22229.cif.gz | 5.2 KB | ||
Others | emd_22229_additional_1.map.gz emd_22229_half_map_1.map.gz emd_22229_half_map_2.map.gz | 98.2 MB 98.2 MB 98.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22229 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22229 | HTTPS FTP |
-Validation report
Summary document | emd_22229_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_22229_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_22229_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | emd_22229_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22229 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22229 | HTTPS FTP |
-Related structure data
Related structure data | 6xkyMC 6xl0C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22229.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map, masked | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_22229_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: unsharpened map, masked
File | emd_22229_additional_1.map | ||||||||||||
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Annotation | unsharpened map, masked | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_22229_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_22229_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : straightened FljK filament
Entire | Name: straightened FljK filament |
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Components |
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-Supramolecule #1: straightened FljK filament
Supramolecule | Name: straightened FljK filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Caulobacter vibrioides NA1000 (bacteria) |
-Macromolecule #1: Flagellin
Macromolecule | Name: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO |
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Source (natural) | Organism: Caulobacter vibrioides (strain NA1000 / CB15N) (bacteria) Strain: NA1000 / CB15N |
Molecular weight | Theoretical: 27.997381 KDa |
Sequence | String: MALNSINTNA GAMIALQNLN GTNSELTTVQ QRINTGKKIA SAKDNGAIWA TAKNQSATAA SMNAVKDSLQ RGQSTIDVAL AAGDTITDL LGKMKEKALA ASDCSLNTAS FNALKSDFDS LRDQIEKAAT SAKFNGVSIA DGSTTKLTFL ANSDGSGFTV N AKTISLAG ...String: MALNSINTNA GAMIALQNLN GTNSELTTVQ QRINTGKKIA SAKDNGAIWA TAKNQSATAA SMNAVKDSLQ RGQSTIDVAL AAGDTITDL LGKMKEKALA ASDCSLNTAS FNALKSDFDS LRDQIEKAAT SAKFNGVSIA DGSTTKLTFL ANSDGSGFTV N AKTISLAG IGLTTTSTFT TAAAAKTMIG TIDTALQTAT NKLASLGTSS VGLDTHLTFV GKLQDSLDAG VGNLVDADLA KE SAKLQSL QTKQQLGVQA LSIANQSSSS ILSLFR UniProtKB: Flagellin |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER / Overall B value: 30.6 / Target criteria: Phenix Refine |
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Output model | PDB-6xky: |