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- EMDB-27059: Cryo-EM structure of the helical E. coli K12 flagellar filament core -

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Basic information

Entry
Database: EMDB / ID: EMD-27059
TitleCryo-EM structure of the helical E. coli K12 flagellar filament core
Map dataCryo-EM structure of the helical E. coli K12 flagellar filament core
Sample
  • Complex: E. coli K12 flagellar filament core
    • Protein or peptide: Flagellin
Biological speciesEscherichia coli K-12 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsSonani RR / Kreutzberger MAB / Sebastian AL / Scharf B / 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 21, 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_27059.png

Downloads & links

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Map

FileDownload / File: emd_27059.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the helical E. coli K12 flagellar filament core
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-0.58662355 - 1.0500444
Average (Standard dev.)0.0017140332 (±0.039424773)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 552.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM structure of the helical E. coli K12 flagellar filament core

Fileemd_27059_half_map_1.map
AnnotationCryo-EM structure of the helical E. coli K12 flagellar filament core
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of the helical E. coli K12 flagellar filament core

Fileemd_27059_half_map_2.map
AnnotationCryo-EM structure of the helical E. coli K12 flagellar filament core
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E. coli K12 flagellar filament core

EntireName: E. coli K12 flagellar filament core
Components
  • Complex: E. coli K12 flagellar filament core
    • Protein or peptide: Flagellin

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Supramolecule #1: E. coli K12 flagellar filament core

SupramoleculeName: E. coli K12 flagellar filament core / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: MG1655

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MAQVINTNSL SLITQNNINK NQSALSSSIE RLSSGLRINS AKDDAAGQAI ANRFTSNIKG LTQAARNAN DGISVAQTTE GALSEINNNL QRVRELTVQA TTGTNSESDL SSIQDEIKSR L DEIDRVSG QTQFNGVNVL AKNGSMKIQV GANDNQTITI DLKQIDAKTL ...String:
MAQVINTNSL SLITQNNINK NQSALSSSIE RLSSGLRINS AKDDAAGQAI ANRFTSNIKG LTQAARNAN DGISVAQTTE GALSEINNNL QRVRELTVQA TTGTNSESDL SSIQDEIKSR L DEIDRVSG QTQFNGVNVL AKNGSMKIQV GANDNQTITI DLKQIDAKTL GLDGFSVKNN DT VTTSAPV TAFGATTTNN IKLTGITLST EAATDTGGTN PASIEGVYTD NGNDYYAKIT GGD NDGKYY AVTVANDGTV TMATGATANA TVTDANTTKA TTITSGGTPV QIDNTAGSAT ANLG AVSLV KLQDSKGNDT DTYALKDTNG NLYAADVNET TGAVSVKTIT YTDSSGAASS PTAVK LGGD DGKTEVVDID GKTYDSADLN GGNLQTGLTA GGEALTAVAN GKTTDPLKAL DDAIAS VDK FRSSLGAVQN RLDSAVTNLN NTTTNLSEAQ SRIQDADYAT EVSNMSKAQI IQQAGNS VL AKANQVPQQV LSLLQG

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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: 7.2
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: 2.2 µm / Nominal defocus min: 1.2 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

Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.832 Å
Applied symmetry - Helical parameters - Δ&Phi: 65.402 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 520264
FSC plot (resolution estimation)

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