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- EMDB-0525: Flagellar cap protein FiD on hook tip from FlaB deletion mutant o... -

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Basic information

Entry
Database: EMDB / ID: EMD-0525
TitleFlagellar cap protein FiD on hook tip from FlaB deletion mutant of B. burgdorferi
Map dataFiD cap on flagellar hook from FlaB deletion mutant. Asymmetric structure. The hook has a helical packing of about 11 subunits per two turns. The cap is asymmetric but close to 5-fold symmetry.
Sample
  • Complex: Flagellar cap protein FiD with hook from FlaB deletion mutant
Biological speciesBorreliella burgdorferi B31 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 32.0 Å
AuthorsQin Z / Liu J
CitationJournal: Mol Microbiol / Year: 2019
Title: Analysis of a flagellar filament cap mutant reveals that HtrA serine protease degrades unfolded flagellin protein in the periplasm of Borrelia burgdorferi.
Authors: Kai Zhang / Zhuan Qin / Yunjie Chang / Jun Liu / Michael G Malkowski / Saimtun Shipa / Li Li / Weigang Qiu / Jing-Ren Zhang / Chunhao Li /
Abstract: Unlike external flagellated bacteria, spirochetes have periplasmic flagella (PF). Very little is known about how PF are assembled within the periplasm of spirochaetal cells. Herein, we report that ...Unlike external flagellated bacteria, spirochetes have periplasmic flagella (PF). Very little is known about how PF are assembled within the periplasm of spirochaetal cells. Herein, we report that FliD (BB0149), a flagellar cap protein (also named hook-associated protein 2), controls flagellin stability and flagellar filament assembly in the Lyme disease spirochete Borrelia burgdorferi. Deletion of fliD leads to non-motile mutant cells that are unable to assemble flagellar filaments and pentagon-shaped caps (10 nm in diameter, 12 nm in length). Interestingly, FlaB, a major flagellin protein of B. burgdorferi, is degraded in the fliD mutant but not in other flagella-deficient mutants (i.e., in the hook, rod, or MS-ring). Biochemical and genetic studies reveal that HtrA, a serine protease of B. burgdorferi, controls FlaB turnover. Specifically, HtrA degrades unfolded but not polymerized FlaB, and deletion of htrA increases the level of FlaB in the fliD mutant. Collectively, we propose that the flagellar cap protein FliD promotes flagellin polymerization and filament growth in the periplasm. Deletion of fliD abolishes this process, which leads to leakage of unfolded FlaB proteins into the periplasm where they are degraded by HtrA, a protease that prevents accumulation of toxic products in the periplasm.
History
DepositionFeb 6, 2019-
Header (metadata) releaseMar 6, 2019-
Map releaseApr 3, 2019-
UpdateJun 26, 2019-
Current statusJun 26, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.082
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.082
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0525.png

Downloads & links

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Map

FileDownload / File: emd_0525.map.gz / Format: CCP4 / Size: 4.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFiD cap on flagellar hook from FlaB deletion mutant. Asymmetric structure. The hook has a helical packing of about 11 subunits per two turns. The cap is asymmetric but close to 5-fold symmetry.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.21 Å/pix.
x 120 pix.
= 624.96 Å		5.21 Å/pix.
x 100 pix.
= 520.8 Å		5.21 Å/pix.
x 100 pix.
= 520.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 5.208 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.082 / Movie #1: 0.082
Minimum - Maximum-0.4241641 - 0.39507207
Average (Standard dev.)0.0010664327 (±0.029770302)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-60
Dimensions100100120
Spacing100100120
CellA: 520.80005 Å / B: 520.80005 Å / C: 624.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.2085.2085.208
M x/y/z100100120
origin x/y/z0.0000.0000.000
length x/y/z520.800520.800624.960
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ304304304
MAP C/R/S123
start NC/NR/NS-50-50-60
NC/NR/NS100100120
D min/max/mean-0.4240.3950.001

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Supplemental data

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Sample components

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Entire : Flagellar cap protein FiD with hook from FlaB deletion mutant

EntireName: Flagellar cap protein FiD with hook from FlaB deletion mutant
Components
  • Complex: Flagellar cap protein FiD with hook from FlaB deletion mutant

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Supramolecule #1: Flagellar cap protein FiD with hook from FlaB deletion mutant

SupramoleculeName: Flagellar cap protein FiD with hook from FlaB deletion mutant
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria) / Strain: B31A

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
Details: BSK-II liquid medium supplemented with 6% rabbit serum
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: OTHER / Number subtomograms used: 1492
ExtractionNumber tomograms: 211 / Number images used: 1492
Final angle assignmentType: NOT APPLICABLE

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