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- EMDB-27065: Cryo-EM helical reconstruction of the S. islandicus REY15A archae... -

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Entry
Database: EMDB / ID: EMD-27065
TitleCryo-EM helical reconstruction of the S. islandicus REY15A archaeal flagellar filament
Map dataCryo-EM helical reconstruction of the S. islandicus REY15A archaeal flagellar filament
Sample
  • Complex: Archaeal flagellar filament
Biological speciesSulfolobus islandicus (acidophilic)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKreutzberger MAB / Liu J / Krupovic M / Egelman EH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Cell / Year: 2022
Title: Convergent evolution in the supercoiling of prokaryotic flagellar filaments.
Authors: Mark A B Kreutzberger / Ravi R Sonani / Junfeng Liu / Sharanya Chatterjee / Fengbin Wang / Amanda L Sebastian / Priyanka Biswas / Cheryl Ewing / Weili Zheng / Frédéric Poly / Gad Frankel / ...Authors: Mark A B Kreutzberger / Ravi R Sonani / Junfeng Liu / Sharanya Chatterjee / Fengbin Wang / Amanda L Sebastian / Priyanka Biswas / Cheryl Ewing / Weili Zheng / Frédéric Poly / Gad Frankel / B F Luisi / Chris R Calladine / Mart Krupovic / Birgit E Scharf / Edward H Egelman /
Abstract: The supercoiling of bacterial and archaeal flagellar filaments is required for motility. Archaeal flagellar filaments have no homology to their bacterial counterparts and are instead homologs of ...The supercoiling of bacterial and archaeal flagellar filaments is required for motility. Archaeal flagellar filaments have no homology to their bacterial counterparts and are instead homologs of bacterial type IV pili. How these prokaryotic flagellar filaments, each composed of thousands of copies of identical subunits, can form stable supercoils under torsional stress is a fascinating puzzle for which structural insights have been elusive. Advances in cryoelectron microscopy (cryo-EM) make it now possible to directly visualize the basis for supercoiling, and here, we show the atomic structures of supercoiled bacterial and archaeal flagellar filaments. For the bacterial flagellar filament, we identify 11 distinct protofilament conformations with three broad classes of inter-protomer interface. For the archaeal flagellar filament, 10 protofilaments form a supercoil geometry supported by 10 distinct conformations, with one inter-protomer discontinuity creating a seam inside of the curve. Our results suggest that convergent evolution has yielded stable superhelical geometries that enable microbial locomotion.
History
DepositionMay 22, 2022-
Header (metadata) releaseSep 7, 2022-
Map releaseSep 7, 2022-
UpdateSep 28, 2022-
Current statusSep 28, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27065.png

Downloads & links

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Map

FileDownload / File: emd_27065.map.gz / Format: CCP4 / Size: 926.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM helical reconstruction of the S. islandicus REY15A archaeal flagellar filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 624 pix.
= 673.92 Å		1.08 Å/pix.
x 624 pix.
= 673.92 Å		1.08 Å/pix.
x 624 pix.
= 673.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.249
Minimum - Maximum-0.35022342 - 0.8755085
Average (Standard dev.)0.0020874608 (±0.025401145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions624624624
Spacing624624624
CellA=B=C: 673.92004 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27065_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM helical reconstruction of the S. islandicus REY15A...

Fileemd_27065_half_map_1.map
AnnotationCryo-EM helical reconstruction of the S. islandicus REY15A archaeal flagellar filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM helical reconstruction of the S. islandicus REY15A...

Fileemd_27065_half_map_2.map
AnnotationCryo-EM helical reconstruction of the S. islandicus REY15A archaeal flagellar filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Archaeal flagellar filament

EntireName: Archaeal flagellar filament
Components
  • Complex: Archaeal flagellar filament

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Supramolecule #1: Archaeal flagellar filament

SupramoleculeName: Archaeal flagellar filament / type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Sulfolobus islandicus (acidophilic) / Strain: REY15A

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.485 Å
Applied symmetry - Helical parameters - Δ&Phi: 107.938 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51914
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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