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- EMDB-27008: Cryo-EM structure of the supercoiled EPEC H6 flagellar filament c... -

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Basic information

Entry
Database: EMDB / ID: EMD-27008
TitleCryo-EM structure of the supercoiled EPEC H6 flagellar filament core Curly I waveform
Map data
Sample
  • Complex: Bacterial flagellar filament core
    • Protein or peptide: Flagellin
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
Flagellin, H7-serospecific domain / Flagellin protein / 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 (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKreutzberger MA / Chatterjee S / Frankel G / 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 18, 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_27008.png

Downloads & links

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Map

FileDownload / File: emd_27008.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.136
Minimum - Maximum-0.5253244 - 0.75546974
Average (Standard dev.)0.0029835922 (±0.031163929)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 414.72003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27008_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27008_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacterial flagellar filament core

EntireName: Bacterial flagellar filament core
Components
  • Complex: Bacterial flagellar filament core
    • Protein or peptide: Flagellin

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Supramolecule #1: Bacterial flagellar filament core

SupramoleculeName: Bacterial flagellar filament core / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: EPEC O127:H6

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 33 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 56.342008 KDa
SequenceString: MAQVINTNSL SLITQNNINK NQSALSSSIE RLSSGLRINS AKDDAAGQAI ANRFTSNIKG LTQAARNAND GISVAQTTEG ALSEINNNL QRIRELTVQA STGTNSDSDL DSIQDEIKSR LDEIDRVSGQ TQFNGVNVLA KDGSMKIQVG ANDGQTITID L KKIDSDTL ...String:
MAQVINTNSL SLITQNNINK NQSALSSSIE RLSSGLRINS AKDDAAGQAI ANRFTSNIKG LTQAARNAND GISVAQTTEG ALSEINNNL QRIRELTVQA STGTNSDSDL DSIQDEIKSR LDEIDRVSGQ TQFNGVNVLA KDGSMKIQVG ANDGQTITID L KKIDSDTL GLNGFNVNGK GETANTAATL KDMSGFTAAA APGGTVGVTQ YTDKSAVASS VDILNAVAGA DGNKVTTSAD VG FGTPAAA VTYTYNKDTN SYSAASDDIS SANLAAFLNP QARDTTKATV TIGGKDQDVN IDKSGNLTAA DDGAVLYMDA TGN LTKNNA GGDTQATLAK VATATGAKAA TIQTDKGTFT SDGTAFDGAS MSIDANTFAN AVKNDTYTAT VGAKTYSVTT GSAA ADTAY MSNGVLSDTP PTYYAQADGS ITTTEDAAAG KLVYKGSDGK LTTDTTSKAE STSDPLAALD DAISQIDKFR SSLGA VQNR LDSAVTNLNN TTTNLSEAQS RIQDADYATE VSNMSKAQII QQAGNSVLAK ANQVPQQVLS LLQG

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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: 6.5
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

Startup modelType of model: EMDB MAP
EMDB ID:

25213

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.33 CUT-OFF / Number images used: 97477

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