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- EMDB-8179: Campylobacter Hook -

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Basic information

Entry
Database: EMDB / ID: EMD-8179
TitleCampylobacter Hook
Map data
Sample
  • Organelle or cellular component: helical assembly of FlgE (flagellar hook)
    • Protein or peptide: Campylobacter hook FlgE
Function / homology
Function and homology information


bacterial-type flagellum organization / bacterial-type flagellum basal body / bacterial-type flagellum-dependent cell motility
Similarity search - Function
Flagellar hook FlgE / Flagellar hook protein FlgE, D3 domain / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, N-terminal ...Flagellar hook FlgE / Flagellar hook protein FlgE, D3 domain / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, N-terminal / Flagellar basal-body/hook protein, C-terminal domain / Flagella basal body rod protein / Flagellar basal body rod FlgEFG protein C-terminal
Similarity search - Domain/homology
Flagellar hook protein FlgE
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni 81116 (Campylobacter)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMatsunami H / Wolf M / Samatey F
CitationJournal: Nat Commun / Year: 2016
Title: Complete structure of the bacterial flagellar hook reveals extensive set of stabilizing interactions.
Authors: Hideyuki Matsunami / Clive S Barker / Young-Ho Yoon / Matthias Wolf / Fadel A Samatey /
Abstract: The bacterial flagellar hook is a tubular helical structure made by the polymerization of multiple copies of a protein, FlgE. Here we report the structure of the hook from Campylobacter jejuni by ...The bacterial flagellar hook is a tubular helical structure made by the polymerization of multiple copies of a protein, FlgE. Here we report the structure of the hook from Campylobacter jejuni by cryo-electron microscopy at a resolution of 3.5 Å. On the basis of this structure, we show that the hook is stabilized by intricate inter-molecular interactions between FlgE molecules. Extra domains in FlgE, found only in Campylobacter and in related bacteria, bring more stability and robustness to the hook. Functional experiments suggest that Campylobacter requires an unusually strong hook to swim without its flagella being torn off. This structure reveals details of the quaternary organization of the hook that consists of 11 protofilaments. Previous study of the flagellar filament of Campylobacter by electron microscopy showed its quaternary structure made of seven protofilaments. Therefore, this study puts in evidence the difference between the quaternary structures of a bacterial filament and its hook.
History
DepositionMay 13, 2016-
Header (metadata) releaseNov 16, 2016-
Map releaseNov 16, 2016-
UpdateNov 16, 2016-
Current statusNov 16, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5jxl
  • Surface level: 2.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5jxl
  • Surface level: 2.4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5jxl
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8179.png

Downloads & links

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Map

FileDownload / File: emd_8179.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.4 / Movie #1: 2.4
Minimum - Maximum-5.6622233 - 9.308794000000001
Average (Standard dev.)0.000000000384276 (±1.)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z324.000324.000324.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ329329329
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-5.6629.3090.000

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Supplemental data

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Sample components

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Entire : helical assembly of FlgE (flagellar hook)

EntireName: helical assembly of FlgE (flagellar hook)
Components
  • Organelle or cellular component: helical assembly of FlgE (flagellar hook)
    • Protein or peptide: Campylobacter hook FlgE

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Supramolecule #1: helical assembly of FlgE (flagellar hook)

SupramoleculeName: helical assembly of FlgE (flagellar hook) / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Campylobacter jejuni subsp. jejuni 81116 (Campylobacter)

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Macromolecule #1: Campylobacter hook FlgE

MacromoleculeName: Campylobacter hook FlgE / type: protein_or_peptide / ID: 1
Details: cju:C8J_1629 hypothetical protein; K02390 flagellar hook protein FlgE (A)
Enantiomer: LEVO
Source (natural)Organism: Campylobacter jejuni subsp. jejuni 81116 (Campylobacter)
SequenceString: MRSLWSGVSG LQAHQVAMDV EGNNISNVNT TGFKYSRADF GTMFSQTVKI ATAPTDGRG GSNPLQIGLG VSVSSTTRIH SQGSVQTTDK NTDVAINGDG FFMVSDDGGL TNYLTRSGDF KLDAYGNFV NNAGFVVQGW NINWDDQTID SSRTPQNIFI DPGMHIPAAK ...String:
MRSLWSGVSG LQAHQVAMDV EGNNISNVNT TGFKYSRADF GTMFSQTVKI ATAPTDGRG GSNPLQIGLG VSVSSTTRIH SQGSVQTTDK NTDVAINGDG FFMVSDDGGL TNYLTRSGDF KLDAYGNFV NNAGFVVQGW NINWDDQTID SSRTPQNIFI DPGMHIPAAK STEVAIKANL N SGLNIGTS SRNLYALDSV HGWNTKTQRA EDENDTGTTQ FYTTSKNSVE VTEKGVDAGA LF NANGTGL NLRDGQGIWV SYADAKFTTD RANGANVFDP NLTVAQQNNV IFWGNKDIAV TLD INLNGV RIQNDNIRSL DEAIAYINTF TAPTDTRDGT GVKAVKKADG SGIEFVNNNA DGTT DNMKN IDLTVNVGNS AGERNTINYN ANTGVFSPQG GNLTTAQNDT DWIAGAAQAG QPQNV KVVT AHKYIYSSNP VTIPPMINPD GGPAFQPNNG NRPTDPASAN YWDAIQGSLK NTTERT FRT TEDLRELLQR DARYGVDYNG SGIIDNATPT FDANDINQAV KVVVTENGNF AISNANE TS TIPANAGAGA GAATTNPKNM SFNITAYSNK QGTVSTNDAF TKIFKAFDGP LVIGNQIK E SEQLKLSAFS AGLEIYDSLG SKHTLEVQFV KQSTTQDGGN EWQMIIRVPE PAEINTTGE GPTNIIVGTA RFNNDGSLAN YTPKTINFSP NNGAAPNQQI KLSFGTSGSN DGLVSSNSAS TLTGQATDG YTSGNLKPDA IRVDDKGNIL GEFTNGKTFA VAKIAMASVA NNSGLEEIGG N LFKVTANS GNIVVGEAGT GGRGEMKTSA LEMSNVDLSR SLTELIIIQR GYQANSKTIS TS DQMLQTL IQLKQ

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 8 / Component - Concentration: 10.0 mM / Component - Formula: Tris-HCl / Component - Name: Tris Hydrochloride / Details: EDTA, Triton X-100
GridModel: Protochips C-Flat CF-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 30.0 nm / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 1e-05 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 280 K / Instrument: GATAN CRYOPLUNGE 3
Details: blotting from both sides, Whatman #40 filter paper, 25 seconds blot time.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 63.0 K / Max: 70.0 K
Detailsparallel illumination
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-5 / Number grids imaged: 1 / Number real images: 504 / Average exposure time: 1.5 sec. / Average electron dose: 2.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 129629 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Detailsfirst 5 image frames were aligned for drift correction and summed. Summed images were normalized.
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.185 Å
Applied symmetry - Helical parameters - Δ&Phi: 64.34 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: segrefinethreed (ver. 0.83) / Software - details: SPRING package / Number images used: 49884
CTF correctionSoftware: (Name: ctffind3 (ver. 3.5), ctftilt (ver. 1.7)) / Details: SPRING v0.83
Segment selectionNumber selected: 70477 / Software - Name: e2helixboxer.py (ver. 2.12)
Startup modelType of model: NONE / Details: from class averages
Final angle assignmentType: NOT APPLICABLE / Software - Name: segrefinethreed (ver. 0.83) / Software - details: SPRING package

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Atomic model buiding 1

Initial modelPDB ID:

5az4


Chain - Chain ID: A / Details: 5JXL
Detailsside chains included, default parameters
RefinementSpace: REAL / Protocol: BACKBONE TRACE / Overall B value: 120 / Target criteria: CC
Output model

PDB-5jxl:
Cryo-EM structure of the flagellar hook of Campylobacter jejuni

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