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- PDB-6xl0: Caulobacter crescentus FljK filament -

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Basic information

Entry
Database: PDB / ID: 6xl0
TitleCaulobacter crescentus FljK filament
ComponentsFlagellin
KeywordsSTRUCTURAL PROTEIN / flagellum / flagellin / filament / helical / Caulobacter / motility
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 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsMontemayor, E.J. / Ploscariu, N.T. / Sanchez, J.C. / Parrell, D. / Dillard, R.S. / Shebelut, C.W. / Ke, Z. / Guerrero-Ferreira, R.C. / Wright, E.R.
Funding support United States, 6items
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, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.title / _citation.year
Revision 1.2Jun 9, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Jul 14, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.4Jul 28, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.5Aug 4, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Flagellin
B: Flagellin
C: Flagellin
D: Flagellin
E: Flagellin
F: Flagellin
G: Flagellin
H: Flagellin
I: Flagellin
J: Flagellin
K: Flagellin
L: Flagellin
M: Flagellin
N: Flagellin
O: Flagellin
P: Flagellin
Q: Flagellin
R: Flagellin
S: Flagellin
T: Flagellin


Theoretical massNumber of molelcules
Total (without water)560,44720
Polymers560,44720
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"
d_11ens_1chain "K"
d_12ens_1chain "L"
d_13ens_1chain "M"
d_14ens_1chain "N"
d_15ens_1chain "O"
d_16ens_1chain "P"
d_17ens_1chain "Q"
d_18ens_1chain "R"
d_19ens_1chain "S"
d_20ens_1chain "T"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAPHEA1 - 271
d_21ens_1ALAPHEB1 - 271
d_31ens_1ALAPHEC1 - 271
d_41ens_1ALAPHED1 - 271
d_51ens_1ALAPHEE1 - 271
d_61ens_1ALAPHEF1 - 271
d_71ens_1ALAPHEG1 - 271
d_81ens_1ALAPHEH1 - 271
d_91ens_1ALAPHEI1 - 271
d_101ens_1ALAPHEJ1 - 271
d_111ens_1ALAPHEK1 - 271
d_121ens_1ALAPHEL1 - 271
d_131ens_1ALAPHEM1 - 271
d_141ens_1ALAPHEN1 - 271
d_151ens_1ALAPHEO1 - 271
d_161ens_1ALAPHEP1 - 271
d_171ens_1ALAPHEQ1 - 271
d_181ens_1ALAPHER1 - 271
d_191ens_1ALAPHES1 - 271
d_201ens_1ALAPHET1 - 271

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Components

#1: Protein
Flagellin /


Mass: 28022.365 Da / Num. of mol.: 20 / Source method: isolated from a natural source
Source: (natural) Caulobacter vibrioides (strain NA1000 / CB15N) (bacteria)
Strain: NA1000 / CB15N / References: UniProt: A0A0H3C7K6, UniProt: P18913*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: FljK filament / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Caulobacter vibrioides NA1000 (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18_3861refinement
PHENIX1.18_3861refinement
EM software
IDNameVersionCategory
4RELION3.1CTF correction
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 65.3 ° / Axial rise/subunit: 4.83 Å / Axial symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77146 / Symmetry type: HELICAL
Atomic model buildingB value: 50.4 / Protocol: OTHER / Space: REAL / Target criteria: Phenix Refine
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 50.38 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007939020
ELECTRON MICROSCOPYf_angle_d0.806452820
ELECTRON MICROSCOPYf_chiral_restr0.04666800
ELECTRON MICROSCOPYf_plane_restr0.00396760
ELECTRON MICROSCOPYf_dihedral_angle_d3.715460
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.000699634409261
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.000709280781731
ens_1d_4AELECTRON MICROSCOPYNCS constraints0.000700656163027
ens_1d_5AELECTRON MICROSCOPYNCS constraints0.000706262025354
ens_1d_6AELECTRON MICROSCOPYNCS constraints0.000705814770367
ens_1d_7AELECTRON MICROSCOPYNCS constraints0.000712864092622
ens_1d_8AELECTRON MICROSCOPYNCS constraints0.000704268115374
ens_1d_9AELECTRON MICROSCOPYNCS constraints0.000696250620864
ens_1d_10AELECTRON MICROSCOPYNCS constraints0.000716680984255
ens_1d_11AELECTRON MICROSCOPYNCS constraints0.0720964314015
ens_1d_12AELECTRON MICROSCOPYNCS constraints0.000706272036274
ens_1d_13AELECTRON MICROSCOPYNCS constraints0.000717661865174
ens_1d_14AELECTRON MICROSCOPYNCS constraints0.00071186049376
ens_1d_15AELECTRON MICROSCOPYNCS constraints0.000700357598441
ens_1d_16AELECTRON MICROSCOPYNCS constraints0.0720123521274
ens_1d_17AELECTRON MICROSCOPYNCS constraints0.000698456471252
ens_1d_18AELECTRON MICROSCOPYNCS constraints0.000699230587182
ens_1d_19AELECTRON MICROSCOPYNCS constraints0.0720893943291
ens_1d_20AELECTRON MICROSCOPYNCS constraints0.000706751619844

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