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- EMDB-10244: Structure of the native C. jejuni flagellum filament -

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Basic information

Entry
Database: EMDB / ID: EMD-10244
TitleStructure of the native C. jejuni flagellum filament
Map dataStructure of the native C.jejuni filament
Sample
  • Complex: Flagellum filament
    • Protein or peptide: FlaA
    • Protein or peptide: FlaB
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
Flagellin hook, IN motif / Flagellin hook IN motif / Flagellin, C-terminal domain, subdomain 2 / 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 A / Flagellin B
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
Methodhelical reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsAl-Otaibi NS / 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 22, 2019-
Header (metadata) releaseJun 24, 2020-
Map releaseJun 24, 2020-
UpdateJul 8, 2020-
Current statusJul 8, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10244.png

Downloads & links

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Map

FileDownload / File: emd_10244.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the native C.jejuni filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.03 Å/pix.
x 300 pix.
= 609. Å		2.03 Å/pix.
x 300 pix.
= 609. Å		2.03 Å/pix.
x 300 pix.
= 609. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.07370541 - 0.14968404
Average (Standard dev.)0.001277308 (±0.010652169)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 609.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.032.032.03
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z609.000609.000609.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0740.1500.001

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Supplemental data

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Sample components

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Entire : Flagellum filament

EntireName: Flagellum filament
Components
  • Complex: Flagellum filament
    • Protein or peptide: FlaA
    • Protein or peptide: FlaB

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Supramolecule #1: Flagellum filament

SupramoleculeName: Flagellum filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Campylobacter jejuni (Campylobacter)

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Macromolecule #1: FlaA

MacromoleculeName: FlaA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Campylobacter jejuni (Campylobacter)
SequenceString: MGFRINTNVA ALNAKANSDL NAKSLDASLS RLSSGLRINS AADDASGMAI ADSLRSQANT LGQAISNGND ALGILQTAD KAMDEQLKIL DTIKTKATQA AQDGQSLKTR TMLQADINKL MEELDNIANT TSFNGKQLLS G NFTNQEFQ IGASSNQTVK ATIGATQSSK ...String:
MGFRINTNVA ALNAKANSDL NAKSLDASLS RLSSGLRINS AADDASGMAI ADSLRSQANT LGQAISNGND ALGILQTAD KAMDEQLKIL DTIKTKATQA AQDGQSLKTR TMLQADINKL MEELDNIANT TSFNGKQLLS G NFTNQEFQ IGASSNQTVK ATIGATQSSK IGVTRFETGA QSFTSGVVGL TIKNYNGIED FKFDNVVIST SV GTGLGAL AEEINKSADK TGVRATYDVK TTGVYAIKEG TTSQEFAING VTIGKIEYKD GDGNGSLISA INA VKDTTG VQASKDENGK LVLTSADGRG IKITGDIGVG SGILANQKEN YGRLSLVKND GRDINISGTN LSAI GMGTT DMISQSSVSL RESKGQISAT NADAMGFNSY KGGGKFVFTQ NVSSISAFMS AQGSGFSRGS GFSVG SGKN LSVGLSQGIQ IISSAASMSN TYVVSAGSGF SSGSGNSQFA ALKTTAANTT DETAGVTTLK GAMAVM DIA ETAITNLDQI RADIGSIQNQ VTSTINNITV TQVNVKAAES QIRDVDFASE SANYSKANIL AQSGSYA MA QANSSQQNVL RLLQ

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Macromolecule #2: FlaB

MacromoleculeName: FlaB / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Campylobacter jejuni (Campylobacter)
SequenceString: MGFRINTNIG ALNAHANSVV NSNELDKSLS RLSSGLRINS AADDASGMAI ADSLRSQAAT LGQAINNGND AIGILQTAD KAMDEQLKIL DTIKTKATQA AQDGQSLKTR TMLQADINKL MEELDNIANT TSFNGKQLLS G NFTNQEFQ IGASSNQTVK ATIGATQSSK ...String:
MGFRINTNIG ALNAHANSVV NSNELDKSLS RLSSGLRINS AADDASGMAI ADSLRSQAAT LGQAINNGND AIGILQTAD KAMDEQLKIL DTIKTKATQA AQDGQSLKTR TMLQADINKL MEELDNIANT TSFNGKQLLS G NFTNQEFQ IGASSNQTVK ATIGATQSSK IGVTRFETGA QSFTSGVVGL TIKNYNGIED FKFDNVVIST SV GTGLGAL AEEINKSADK TGVRATYDVK TTGVYAIKEG TTSQDFAING VAIGQINYKD GDNNGQLVSA INA VKDTTG VQASKDENGK LVLTSADGRG IKITGDIGVG SGILANQKEN YGRLSLVKND GRDINISGTN LSAI GMGTT DMISQSSVSL RESKGQISAT NADAMGFNSY KGGGKFVFTQ NVSSISAFMS AQGSGFSRGS GFSVG SGKN LSVGLSQGIQ IISSAASMSN TYVVSAGSGF SSGSGNSQFA ALKTTAANTT DETAGVTTLK GAMAVM DIA ETAITNLDQI RADIGSVQNQ LQVTINNITV TQVNVKAAES TIRDVDFASE SANFSKYNIL AQSGSYA MS QANAVQQNVL KLLQ

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 65.4 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 254041
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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