Japan Agency for Medical Research and Development (AMED)
JP19am0101117,JP17pc0101020
Japan
Citation
Journal: Nat Commun / Year: 2021 Title: Structure of the molecular bushing of the bacterial flagellar motor. Authors: Tomoko Yamaguchi / Fumiaki Makino / Tomoko Miyata / Tohru Minamino / Takayuki Kato / Keiichi Namba / Abstract: The basal body of the bacterial flagellum is a rotary motor that consists of several rings (C, MS and LP) and a rod. The LP ring acts as a bushing supporting the distal rod for its rapid and stable ...The basal body of the bacterial flagellum is a rotary motor that consists of several rings (C, MS and LP) and a rod. The LP ring acts as a bushing supporting the distal rod for its rapid and stable rotation without much friction. Here, we use electron cryomicroscopy to describe the LP ring structure around the rod, at 3.5 Å resolution, from Salmonella Typhimurium. The structure shows 26-fold rotational symmetry and intricate intersubunit interactions of each subunit with up to six partners, which explains the structural stability. The inner surface is charged both positively and negatively. Positive charges on the P ring (the part of the LP ring that is embedded within the peptidoglycan layer) presumably play important roles in its initial assembly around the rod with a negatively charged surface.
#262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (4)
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Assembly
Deposited unit
A: Flagellar P-ring protein B: Flagellar P-ring protein C: Flagellar P-ring protein D: Flagellar P-ring protein E: Flagellar P-ring protein F: Flagellar P-ring protein G: Flagellar P-ring protein H: Flagellar P-ring protein I: Flagellar P-ring protein J: Flagellar P-ring protein K: Flagellar P-ring protein L: Flagellar P-ring protein M: Flagellar P-ring protein N: Flagellar P-ring protein O: Flagellar P-ring protein P: Flagellar P-ring protein Q: Flagellar P-ring protein R: Flagellar P-ring protein S: Flagellar P-ring protein T: Flagellar P-ring protein U: Flagellar P-ring protein V: Flagellar P-ring protein W: Flagellar P-ring protein X: Flagellar P-ring protein Y: Flagellar P-ring protein Z: Flagellar P-ring protein a: Flagellar L-ring protein b: Flagellar L-ring protein c: Flagellar L-ring protein d: Flagellar L-ring protein e: Flagellar L-ring protein f: Flagellar L-ring protein g: Flagellar L-ring protein h: Flagellar L-ring protein i: Flagellar L-ring protein j: Flagellar L-ring protein k: Flagellar L-ring protein l: Flagellar L-ring protein m: Flagellar L-ring protein n: Flagellar L-ring protein o: Flagellar L-ring protein p: Flagellar L-ring protein q: Flagellar L-ring protein r: Flagellar L-ring protein s: Flagellar L-ring protein t: Flagellar L-ring protein u: Flagellar L-ring protein v: Flagellar L-ring protein w: Flagellar L-ring protein x: Flagellar L-ring protein y: Flagellar L-ring protein z: Flagellar L-ring protein
Average exposure time: 10 sec. / Electron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 12759
EM imaging optics
Energyfilter name: In-column Omega Filter
Image scans
Movie frames/image: 50 / Used frames/image: 1-50
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Processing
EM software
ID
Name
Version
Category
Details
2
RELION
3
imageacquisition
beta-2
4
Gctf
1.06
CTFcorrection
7
PHENIX
1.13
modelfitting
8
Coot
0.8.9.1
modelfitting
9
UCSF Chimera
1.11.2
modelfitting
11
PHENIX
1.13
modelrefinement
12
Coot
0.8.9.1
modelrefinement
13
RELION
3.0 beta-2
initialEulerassignment
14
RELION
3.0 beta-2
finalEulerassignment
15
RELION
3.0 beta-2
classification
16
RELION
3.0 beta-2
3Dreconstruction
CTF correction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selection
Num. of particles selected: 64418 Details: particles were picked up by YOLOPick.py (in-house python program)
Symmetry
Point symmetry: C26 (26 fold cyclic)
3D reconstruction
Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10802 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT
Atomic model building
B value: 38 / Protocol: OTHER / Space: REAL
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