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- EMDB-27026: Cryo-EM structure of the supercoiled S. islandicus REY15A archaea... -

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Basic information

Entry
Database: EMDB / ID: EMD-27026
TitleCryo-EM structure of the supercoiled S. islandicus REY15A archaeal flagellar filament
Map data
Sample
  • Complex: Archaeal flagellar filament
    • Protein or peptide: Flagellin
Function / homologyarchaeal-type flagellum / Flagellin/pilin, N-terminal / Flagellin, archaea / Archaebacterial flagellin / archaeal or bacterial-type flagellum-dependent cell motility / membrane => GO:0016020 / structural molecule activity / Flagellin
Function and homology information
Biological speciesSulfolobus islandicus (acidophilic) / Sulfolobus islandicus REY15A (acidophilic)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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 19, 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_27026.png

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Map

FileDownload / File: emd_27026.map.gz / Format: CCP4 / Size: 926.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.112
Minimum - Maximum-0.781979 - 1.3217156
Average (Standard dev.)0.001939982 (±0.027488664)
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_27026_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_27026_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27026_half_map_2.map
Projections & Slices
AxesZYX

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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
    • Protein or peptide: Flagellin

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Supramolecule #1: Archaeal flagellar filament

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

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic) / Strain: REY15A
Molecular weightTheoretical: 33.1335 KDa
SequenceString: MNTKKMLKEY NKKVKRKGLA GLDTAIILIA FIITASVLAY VAINMGLFVT QKAKSTINKG EETASTALTL SGSVLYAVNY PSNTRSYWI YFTVSPSSGV SSVELSPSTT AISFTASAEG ISYSNIYEYT LLTVSPSELA NQVYANGQYL DLVNQQTNAG Q TYVYYPNP ...String:
MNTKKMLKEY NKKVKRKGLA GLDTAIILIA FIITASVLAY VAINMGLFVT QKAKSTINKG EETASTALTL SGSVLYAVNY PSNTRSYWI YFTVSPSSGV SSVELSPSTT AISFTASAEG ISYSNIYEYT LLTVSPSELA NQVYANGQYL DLVNQQTNAG Q TYVYYPNP YYALLALNYT LSKIDKVSPS PLYITTTTPS SATQIYPFLA HDNMFTFTLN ISGTLVTYYA FVNQTFAFTY PV AGDPLIG SAIAPAGSVI GVMILFGPDL GSHVFQYQTI TIQITPNIGS PLTISEYVYQ PEGSVSVIG

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.33 CUT-OFF / Number images used: 51914

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