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- PDB-6sih: Structure of bacterial flagellar capping protein FliD -

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Basic information

Entry
Database: PDB / ID: 6sih
TitleStructure of bacterial flagellar capping protein FliD
ComponentsFlagellar hook-associated protein 2
KeywordsTRANSPORT PROTEIN / Flagellum / Flagella / FliD / HAP2 / Campylobacter jejuni / C.jejuni
Function / homology
Function and homology information


bacterial-type flagellum filament cap / bacterial-type flagellum hook / cell adhesion / extracellular region
Similarity search - Function
Flagellar hook-associated protein 2, N-terminal / Flagellar hook-associated protein 2, C-terminal / Flagellar hook-associated protein 2 / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus / Flagellin hook, IN motif / Flagellin hook IN motif
Similarity search - Domain/homology
Flagellar hook-associated protein 2
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsAl-Otaibi, N.S. / Farrell, D. / DiMaio, F. / Bergeron, J.R.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: The cryo-EM structure of the bacterial flagellum cap complex suggests a molecular mechanism for filament elongation.
Authors: Natalie S Al-Otaibi / Aidan J Taylor / Daniel P Farrell / Svetomir B Tzokov / Frank DiMaio / David J Kelly / Julien R C Bergeron /
Abstract: The bacterial flagellum is a remarkable molecular motor, whose primary function in bacteria is to facilitate motility through the rotation of a filament protruding from the bacterial cell. A cap ...The bacterial flagellum is a remarkable molecular motor, whose primary function in bacteria is to facilitate motility through the rotation of a filament protruding from the bacterial cell. A cap complex, consisting of an oligomer of the protein FliD, is localized at the tip of the flagellum, and is essential for filament assembly, as well as adherence to surfaces in some bacteria. However, the structure of the intact cap complex, and the molecular basis for its interaction with the filament, remains elusive. Here we report the cryo-EM structure of the Campylobacter jejuni cap complex, which reveals that FliD is pentameric, with the N-terminal region of the protomer forming an extensive set of contacts across several subunits, that contribute to FliD oligomerization. We also demonstrate that the native C. jejuni flagellum filament is 11-stranded, contrary to a previously published cryo-EM structure, and propose a molecular model for the filament-cap interaction.
History
DepositionAug 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
A: Flagellar hook-associated protein 2
H: Flagellar hook-associated protein 2
B: Flagellar hook-associated protein 2
F: Flagellar hook-associated protein 2
C: Flagellar hook-associated protein 2
G: Flagellar hook-associated protein 2
D: Flagellar hook-associated protein 2
I: Flagellar hook-associated protein 2
E: Flagellar hook-associated protein 2
J: Flagellar hook-associated protein 2


Theoretical massNumber of molelcules
Total (without water)721,59310
Polymers721,59310
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area39720 Å2
ΔGint-302 kcal/mol
Surface area234310 Å2
MethodPISA

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Components

#1: Protein
Flagellar hook-associated protein 2 / HAP2 / Flagellar cap protein


Mass: 72159.305 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: fliD, EC071_02365 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3I4YJR7

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Decamer complex of FliD / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Campylobacter jejuni (Campylobacter) / Strain: 81116
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Calibrated magnification: 36232 X
Image recordingAverage exposure time: 10 sec. / Electron dose: 41 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1223

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00374500
ELECTRON MICROSCOPYf_angle_d0.55134540
ELECTRON MICROSCOPYf_dihedral_angle_d5.32729760
ELECTRON MICROSCOPYf_chiral_restr0.0356010
ELECTRON MICROSCOPYf_plane_restr0.00211400

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