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- EMDB-9122: Flagellar motor averaged map from Borrelia burdorferi reveals the... -

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Entry
Database: EMDB / ID: EMD-9122
TitleFlagellar motor averaged map from Borrelia burdorferi reveals the cytoplasmic ATPase complex
Map dataA recombined map of Borrelia burgdorferi flagellar motor (WT). The top part (collar and stators) and bottom part (C-ring and ATPase complex) have been processed separately.
Sample
  • Organelle or cellular component: Borrelia burgdorferi flagellar motor averaged recombined averaged map. It shows 16-fold symmetry at collar and stators region, 23 spoke linkers, and 6-fold symmetry of the ATPase. The top part (collar and stators) and bottom part (C-ring and ATPase complex) were processed separatedly.
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
Methodsubtomogram averaging / cryo EM / Resolution: 29.0 Å
AuthorsQin Z / Liu J
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesR01AI087949 United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesR01DE023080 United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesR01AI078958 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin DiseasesR01AR060834 United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesR21AI113014 United States
Welch FoundationAU-1714 United States
CitationJournal: PLoS Biol / Year: 2018
Title: Cryo-electron tomography of periplasmic flagella in Borrelia burgdorferi reveals a distinct cytoplasmic ATPase complex.
Authors: Zhuan Qin / Jiagang Tu / Tao Lin / Steven J Norris / Chunhao Li / Md A Motaleb / Jun Liu /
Abstract: Periplasmic flagella are essential for the distinct morphology and motility of spirochetes. A flagella-specific type III secretion system (fT3SS) composed of a membrane-bound export apparatus and a ...Periplasmic flagella are essential for the distinct morphology and motility of spirochetes. A flagella-specific type III secretion system (fT3SS) composed of a membrane-bound export apparatus and a cytosolic ATPase complex is responsible for the assembly of the periplasmic flagella. Here, we deployed cryo-electron tomography (cryo-ET) to visualize the fT3SS machine in the Lyme disease spirochete Borrelia burgdorferi. We show, for the first time, that the cytosolic ATPase complex is attached to the flagellar C-ring through multiple spokes to form the "spoke and hub" structure in B. burgdorferi. This structure not only strengthens structural rigidity of the round-shaped C-ring but also appears to rotate with the C-ring. Our studies provide structural insights into the unique mechanisms underlying assembly and rotation of the periplasmic flagella and may provide the basis for the development of novel therapeutic strategies against several pathogenic spirochetes.
History
DepositionSep 18, 2018-
Header (metadata) releaseOct 17, 2018-
Map releaseOct 17, 2018-
UpdateAug 12, 2020-
Current statusAug 12, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.53
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.53
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9122.png

Downloads & links

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Map

FileDownload / File: emd_9122.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA recombined map of Borrelia burgdorferi flagellar motor (WT). The top part (collar and stators) and bottom part (C-ring and ATPase complex) have been processed separately.
Voxel sizeX=Y=Z: 5.208 Å
Density
Contour LevelBy AUTHOR: 0.53 / Movie #1: 0.53
Minimum - Maximum-0.00000000000 - 1.1191231
Average (Standard dev.)0.09579309 (±0.2061568)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 1041.6001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.2085.2085.208
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z1041.6001041.6001041.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-163-114-126
NX/NY/NZ210124170
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-0.0001.1190.096

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Supplemental data

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Mask #1

Fileemd_9122_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: An averaged map focus on linkers and C-ring,...

Fileemd_9122_additional_1.map
AnnotationAn averaged map focus on linkers and C-ring, showing 23 linkers and 46-fold symmetry of the C-ring. The ATPase is 6-fold symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The original averaged map with a focus on...

Fileemd_9122_additional_2.map
AnnotationThe original averaged map with a focus on the ATPase complex region. The map was not masked or filtered. The feature of the top part (collar and stators) was averaged out.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Borrelia burgdorferi flagellar motor averaged recombined averaged...

EntireName: Borrelia burgdorferi flagellar motor averaged recombined averaged map. It shows 16-fold symmetry at collar and stators region, 23 spoke linkers, and 6-fold symmetry of the ATPase. The top part ...Name: Borrelia burgdorferi flagellar motor averaged recombined averaged map. It shows 16-fold symmetry at collar and stators region, 23 spoke linkers, and 6-fold symmetry of the ATPase. The top part (collar and stators) and bottom part (C-ring and ATPase complex) were processed separatedly.
Components
  • Organelle or cellular component: Borrelia burgdorferi flagellar motor averaged recombined averaged map. It shows 16-fold symmetry at collar and stators region, 23 spoke linkers, and 6-fold symmetry of the ATPase. The top part (collar and stators) and bottom part (C-ring and ATPase complex) were processed separatedly.

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Supramolecule #1: Borrelia burgdorferi flagellar motor averaged recombined averaged...

SupramoleculeName: Borrelia burgdorferi flagellar motor averaged recombined averaged map. It shows 16-fold symmetry at collar and stators region, 23 spoke linkers, and 6-fold symmetry of the ATPase. The top part ...Name: Borrelia burgdorferi flagellar motor averaged recombined averaged map. It shows 16-fold symmetry at collar and stators region, 23 spoke linkers, and 6-fold symmetry of the ATPase. The top part (collar and stators) and bottom part (C-ring and ATPase complex) were processed separatedly.
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Details: Wild-type. Top part and bottom part have different symmetry, and were processed separately from the same group of sub-tomograms.
Source (natural)Organism: Borrelia burgdorferi (Lyme disease spirochete) / Strain: B31 / Organelle: Flagellar motor / Location in cell: cell tip

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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
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 780 / Number images used: 6567 / Method: Subvolume averaging and Classification / Details: i3
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: FSC 0.143 CUT-OFF
Details: It is combined from top map and bottom map. Top had 16-fold symmetry applied. The bottom map was asymmetric.
Number subtomograms used: 4825

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