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- EMDB-10210: Structure of bacterial flagellar capping protein FliD -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-10210
TitleStructure of bacterial flagellar capping protein FliD
Map dataFliDcj full model
Sample
  • Complex: Decamer complex of FliD
    • Protein or peptide: Flagellar hook-associated protein 2
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsAl-Otaibi NS / Farrell D / DiMaio F / Bergeron JRC
Funding support United Kingdom, 1 items
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, 2019-
Header (metadata) releaseMay 27, 2020-
Map releaseMay 27, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 6.9
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6sih
  • Surface level: 6.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10210.png

Downloads & links

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Map

FileDownload / File: emd_10210.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFliDcj full model
Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 6.9 / Movie #1: 6.9
Minimum - Maximum-12.866016 - 24.195026
Average (Standard dev.)0.00000000001 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 386.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z386.400386.400386.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-12.86624.1950.000

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Supplemental data

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Additional map: FliDcj head domain

Fileemd_10210_additional.map
AnnotationFliDcj head domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Decamer complex of FliD

EntireName: Decamer complex of FliD
Components
  • Complex: Decamer complex of FliD
    • Protein or peptide: Flagellar hook-associated protein 2

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Supramolecule #1: Decamer complex of FliD

SupramoleculeName: Decamer complex of FliD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Campylobacter jejuni (Campylobacter) / Strain: 81116
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Flagellar hook-associated protein 2

MacromoleculeName: Flagellar hook-associated protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Campylobacter jejuni (Campylobacter)
Molecular weightTheoretical: 72.159305 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MAFGSLSSLG FGSGVLTQDT IDKLKEAEQK ARIDPYTKKI EENTTKQKDL TEIKTKLLSF QTAVSSLAD ATVFAKRKVV GSISDNPPAS LTVNSGVALQ SMNINVTQLA QKDVYQSKGL ANDSGFVNAN LTGTTDLTFF S NGKEYTVT ...String:
MGSSHHHHHH SSGLVPRGSH MAFGSLSSLG FGSGVLTQDT IDKLKEAEQK ARIDPYTKKI EENTTKQKDL TEIKTKLLSF QTAVSSLAD ATVFAKRKVV GSISDNPPAS LTVNSGVALQ SMNINVTQLA QKDVYQSKGL ANDSGFVNAN LTGTTDLTFF S NGKEYTVT VDKNTTYRDL ADKINEASGG EIVAKIVNTG EKGTPYRLTL TSKETGEDSA ISFYAGKKDA QGQYQSDPEA EN IFSNLGW ELDKTTQTID PAKDKKGYGI KDASLHIQTA QNAEFTLDGI KMFRSSNTVT DLGVGMTLTL NKTGEINFDV QQD FEGVTK AMQDLVDAYN DLVTNLNAAT DYNSETGTKG TLQGISEVNS IRSSILADLF DSQVVDGTTE DANGNKVNTK VMLS MQDFG LSLNDAGTLS FDSSKFEQKV KEDPDSTESF FSNITKYEDI NHTGEVIKQG SLNQYLDSSG TGNKGLDFKP GDFTI VFNN QTYDLSKNSD GTNFKLTGKT EEELLQNLAN HINSKGIEGL KVKVESYDQN GVKGFKLNFS GDGSSDFSIK GNATIL QEL GLSDVNITSK PIEGKGIFSK LKATLQEMTG KDGSITKYDE SLTNDIKSLN TSKDSTQAMI DTRYDTMANQ WLQYESI LN KLNQQLNTVT NMINAANNSN N

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 36232 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1223 / Average exposure time: 10.0 sec. / Average electron dose: 41.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56000
FSC plot (resolution estimation)

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