- EMDB-0525: Flagellar cap protein FiD on hook tip from FlaB deletion mutant o... -
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Open data
ID or keywords:
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Basic information
Entry
Database: EMDB / ID: EMD-0525
Title
Flagellar cap protein FiD on hook tip from FlaB deletion mutant of B. burgdorferi
Map data
FiD 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 species
Borreliella burgdorferi B31 (bacteria)
Method
subtomogram averaging / cryo EM / Resolution: 32.0 Å
Journal: 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
Deposition
Feb 6, 2019
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Header (metadata) release
Mar 6, 2019
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Map release
Apr 3, 2019
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Update
Jun 26, 2019
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Current status
Jun 26, 2019
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_0525.map.gz / Format: CCP4 / Size: 4.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
FiD 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.
Voxel size
X=Y=Z: 5.208 Å
Density
Contour Level
By AUTHOR: 0.082 / Movie #1: 0.082
Minimum - Maximum
-0.4241641 - 0.39507207
Average (Standard dev.)
0.0010664327 (±0.029770302)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
-50
-50
-60
Dimensions
100
100
120
Spacing
100
100
120
Cell
A: 520.80005 Å / B: 520.80005 Å / C: 624.96 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
5.208
5.208
5.208
M x/y/z
100
100
120
origin x/y/z
0.000
0.000
0.000
length x/y/z
520.800
520.800
624.960
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
0
0
0
NX/NY/NZ
304
304
304
MAP C/R/S
1
2
3
start NC/NR/NS
-50
-50
-60
NC/NR/NS
100
100
120
D min/max/mean
-0.424
0.395
0.001
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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
Entire
Name: 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
Supramolecule
Name: Flagellar cap protein FiD with hook from FlaB deletion mutant type: complex / ID: 1 / Parent: 0
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics
Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
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Image processing
Final reconstruction
Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: OTHER / Number subtomograms used: 1492
Extraction
Number tomograms: 211 / Number images used: 1492
Final angle assignment
Type: NOT APPLICABLE
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