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- EMDB-21884: Local refined structure of stator and C-ring interaction region i... -

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Basic information

Entry
Database: EMDB / ID: EMD-21884
TitleLocal refined structure of stator and C-ring interaction region in clockwise rotating delta-cheY3 Borrelia flagellar motor
Map dataLocal refined structure of stator and C-ring interaction region in clockwise rotating %u2206cheY3 Borrelia flagellar motor
Sample
  • Complex: Stator and C-ring interaction region in clockwise rotating delta-cheY3 Borrelia flagellar motor
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
Methodsubtomogram averaging / cryo EM / Resolution: 19.0 Å
AuthorsChang YJ / Liu J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI132818 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI087946 United States
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Molecular mechanism for rotational switching of the bacterial flagellar motor.
Authors: Yunjie Chang / Kai Zhang / Brittany L Carroll / Xiaowei Zhao / Nyles W Charon / Steven J Norris / Md A Motaleb / Chunhao Li / Jun Liu /
Abstract: The bacterial flagellar motor can rotate in counterclockwise (CCW) or clockwise (CW) senses, and transitions are controlled by the phosphorylated form of the response regulator CheY (CheY-P). To ...The bacterial flagellar motor can rotate in counterclockwise (CCW) or clockwise (CW) senses, and transitions are controlled by the phosphorylated form of the response regulator CheY (CheY-P). To dissect the mechanism underlying flagellar rotational switching, we use Borrelia burgdorferi as a model system to determine high-resolution in situ motor structures in cheX and cheY3 mutants, in which motors are locked in either CCW or CW rotation. The structures showed that CheY3-P interacts directly with a switch protein, FliM, inducing a major remodeling of another switch protein, FliG2, and altering its interaction with the torque generator. Our findings lead to a model in which the torque generator rotates in response to an inward flow of H driven by the proton motive force, and conformational changes in FliG2 driven by CheY3-P allow the switch complex to interact with opposite sides of the rotating torque generator, facilitating rotational switching.
History
DepositionApr 29, 2020-
Header (metadata) releaseSep 2, 2020-
Map releaseSep 2, 2020-
UpdateSep 9, 2020-
Current statusSep 9, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21884.png

Downloads & links

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Map

FileDownload / File: emd_21884.map.gz / Format: CCP4 / Size: 17.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refined structure of stator and C-ring interaction region in clockwise rotating %u2206cheY3 Borrelia flagellar motor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.75 Å/pix.
x 240 pix.
= 659.28 Å		2.75 Å/pix.
x 140 pix.
= 384.58 Å		2.75 Å/pix.
x 140 pix.
= 384.58 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: 2.747 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.36687037 - 0.4815557
Average (Standard dev.)0.00001698659 (±0.034022402)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140240
Spacing140140240
CellA: 384.58 Å / B: 384.58 Å / C: 659.27997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.7472.7472.747
M x/y/z140140240
origin x/y/z0.0000.0000.000
length x/y/z384.580384.580659.280
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ500500500
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140240
D min/max/mean-0.3670.4820.000

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Supplemental data

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Sample components

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Entire : Stator and C-ring interaction region in clockwise rotating delta-...

EntireName: Stator and C-ring interaction region in clockwise rotating delta-cheY3 Borrelia flagellar motor
Components
  • Complex: Stator and C-ring interaction region in clockwise rotating delta-cheY3 Borrelia flagellar motor

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Supramolecule #1: Stator and C-ring interaction region in clockwise rotating delta-...

SupramoleculeName: Stator and C-ring interaction region in clockwise rotating delta-cheY3 Borrelia flagellar motor
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Borreliella burgdorferi (Lyme disease spirochete) / 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: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 14066
ExtractionNumber tomograms: 301 / Number images used: 15024
CTF correctionDetails: IMOD ctfphaseflip
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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