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- EMDB-27060: Cryo-EM structure of the supercoiled E. coli K12 flagellar filame... -

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Basic information

Entry
Database: EMDB / ID: EMD-27060
TitleCryo-EM structure of the supercoiled E. coli K12 flagellar filament core, Normal waveform
Map dataCryo-EM structure of the supercoiled E. coli K12 flagellar filament core, Normal waveform
Sample
  • Complex: E. coli K12 flagellar filament core
    • Protein or peptide: Flagellin
KeywordsBacterial motility / flagellar filament / flagellin / STRUCTURAL PROTEIN
Function / homology
Function and homology information


Toll Like Receptor 5 (TLR5) Cascade / MyD88 deficiency (TLR5) / IRAK4 deficiency (TLR5) / MyD88 cascade initiated on plasma membrane / bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
Flagellin D3 / : / Flagellin D3 domain / Flagellin, barrel domain / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 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-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27060.png

Downloads & links

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Map

FileDownload / File: emd_27060.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the supercoiled E. coli K12 flagellar filament core, Normal waveform
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 512 pix.
= 552.96 Å		1.08 Å/pix.
x 512 pix.
= 552.96 Å		1.08 Å/pix.
x 512 pix.
= 552.96 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: 0.25
Minimum - Maximum-0.40333664 - 0.8507503
Average (Standard dev.)0.0017729368 (±0.042279616)
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 supercoiled E. coli K12...

Fileemd_27060_half_map_1.map
AnnotationCryo-EM structure of the supercoiled E. coli K12 flagellar filament core, Normal waveform
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of the supercoiled E. coli K12...

Fileemd_27060_half_map_2.map
AnnotationCryo-EM structure of the supercoiled E. coli K12 flagellar filament core, Normal waveform
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 / 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 / Number of copies: 55 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 51.330582 KDa
SequenceString: MAQVINTNSL SLITQNNINK NQSALSSSIE RLSSGLRINS AKDDAAGQAI ANRFTSNIKG LTQAARNAND GISVAQTTEG ALSEINNNL QRVRELTVQA TTGTNSESDL SSIQDEIKSR LDEIDRVSGQ TQFNGVNVLA KNGSMKIQVG ANDNQTITID L KQIDAKTL ...String:
MAQVINTNSL SLITQNNINK NQSALSSSIE RLSSGLRINS AKDDAAGQAI ANRFTSNIKG LTQAARNAND GISVAQTTEG ALSEINNNL QRVRELTVQA TTGTNSESDL SSIQDEIKSR LDEIDRVSGQ TQFNGVNVLA KNGSMKIQVG ANDNQTITID L KQIDAKTL GLDGFSVKNN DTVTTSAPVT AFGATTTNNI KLTGITLSTE AATDTGGTNP ASIEGVYTDN GNDYYAKITG GD NDGKYYA VTVANDGTVT MATGATANAT VTDANTTKAT TITSGGTPVQ IDNTAGSATA NLGAVSLVKL QDSKGNDTDT YAL KDTNGN LYAADVNETT GAVSVKTITY TDSSGAASSP TAVKLGGDDG KTEVVDIDGK TYDSADLNGG NLQTGLTAGG EALT AVANG KTTDPLKALD DAIASVDKFR SSLGAVQNRL DSAVTNLNNT TTNLSEAQSR IQDADYATEV SNMSKAQIIQ QAGNS VLAK ANQVPQQVLS LLQG

UniProtKB: Flagellin

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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: 7.2
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: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49279
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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