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- EMDB-26995: Cryo-EM helical reconstruction of the EPEC H6 Curly I flagellar core -

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Basic information

Entry
Database: EMDB / ID: EMD-26995
TitleCryo-EM helical reconstruction of the EPEC H6 Curly I flagellar core
Map data
Sample
  • Complex: Bacterial flagellar filament core
    • Protein or peptide: Bacterial flagellin
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKreutzberger MAB / 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 16, 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_26995.png

Downloads & links

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Map

FileDownload / File: emd_26995.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.146
Minimum - Maximum-0.37101597 - 0.5996536
Average (Standard dev.)0.00376484 (±0.03353689)
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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Mask #1

Fileemd_26995_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_26995_half_map_1.map
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Half map: #2

Fileemd_26995_half_map_2.map
Projections & Slices
AxesZYX

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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: Bacterial 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: Bacterial flagellin

MacromoleculeName: Bacterial flagellin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: EPEC O127:H6
SequenceString: MAQVINTNSL SLITQNNINK NQSALSSSIE RLSSGLRINS AKDDAAGQAI ANRFTSNIKG LTQAARNAN DGISVAQTTE GALSEINNNL QRIRELTVQA STGTNSDSDL DSIQDEIKSR L DEIDRVSG QTQFNGVNVL AKDGSMKIQV GANDGQTITI DLKKIDSDTL ...String:
MAQVINTNSL SLITQNNINK NQSALSSSIE RLSSGLRINS AKDDAAGQAI ANRFTSNIKG LTQAARNAN DGISVAQTTE GALSEINNNL QRIRELTVQA STGTNSDSDL DSIQDEIKSR L DEIDRVSG QTQFNGVNVL AKDGSMKIQV GANDGQTITI DLKKIDSDTL GLNGFNVNGK GE TANTAAT LKDMSGFTAA AAPGGTVGVT QYTDKSAVAS SVDILNAVAG ADGNKVTTSA DVG FGTPAA AVTYTYNKDT NSYSAASDDI SSANLAAFLN PQARDTTKAT VTIGGKDQDV NIDK SGNLT AADDGAVLYM DATGNLTKNN AGGDTQATLA KVATATGAKA ATIQTDKGTF TSDGT AFDG ASMSIDANTF ANAVKNDTYT ATVGAKTYSV TTGSAAADTA YMSNGVLSDT PPTYYA QAD GSITTTEDAA AGKLVYKGSD GKLTTDTTSK AESTSDPLAA LDDAISQIDK FRSSLGA VQ NRLDSAVTNL NNTTTNLSEA QSRIQDADYA TEVSNMSKAQ IIQQAGNSVL AKANQVPQ Q VLSLLQG

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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: 6.5
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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.813 Å
Applied symmetry - Helical parameters - Δ&Phi: 65.539 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 269269
Startup modelType of model: EMDB MAP
EMDB ID:

25213

Final angle assignmentType: NOT APPLICABLE

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