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- EMDB-70987: CryoEM structure of hook from Shewanella oneidensis -

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Basic information

Entry
Database: EMDB / ID: EMD-70987
TitleCryoEM structure of hook from Shewanella oneidensis
Map dataCryoEM structure of the hook from Shewanella oneidensis. The above primary density map was upsampled from a pixel size of 1.1 A to 1.0 A and flipped to the correct handedness.
Sample
  • Complex: Hook
KeywordsHook / Shewanella oneidensis / STRUCTURAL PROTEIN
Biological speciesShewanella oneidensis MR-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.18 Å
AuthorsLou Q / Fan HC / Liu Y / Miller JF / Huang Y / Zhou ZH
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
National Institutes of Health/Office of the Director1S10OD018111 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
CitationJournal: ACS Nano / Year: 2025
Title: Curvature Generation and Engineering Principles from Multi-flagellin Flagellum.
Authors: Qing Lou / Hongcheng Fan / Yang Liu / Jeff F Miller / Yu Huang / Z Hong Zhou /
Abstract: Motility driven by nanoscale flagella is vital to microbial survival and spread in fluid and structured environments. The absence of native flagellum structures, however, has limited our ...Motility driven by nanoscale flagella is vital to microbial survival and spread in fluid and structured environments. The absence of native flagellum structures, however, has limited our understanding of the mechanisms of microbial motility, hindering efforts to engineer microbe-based microbots for applications. Here, by cryogenic electron tomography (cryoET) and microscopy (cryoEM), we determined the structural basis of motility driven by the single flagellum anchored to one pole of MR-1 (), an electrogenic bacterium commonly used in biotechnology. The structures of the curved flagellum, representing the conformation during motion, are captured, allowing delineation of molecular interactions among the subunits of its three components─filament, hook, and hook-filament junction. The structures of the filament, i.e., the propeller, reveal varying compositions of the flagellin isoforms FlaA and FlaB throughout the filament. Distinct inter-subunit interactions along the 5-start direction are identified at residues 129 and 134, which are the major determinants of functional differences in motility for the two isoforms. The hook─the universal joint─has a significantly larger curvature than that of the filament, despite both containing 11 curvature-defining conformers of their subunits. Transition between the propeller and the universal joint is mediated by the hook-filament junction, composed of 11 subunits of FlgK and FlgL, reconciling the incompatibility between the filament and the hook. Correlating these compositional and structural transitions with varying levels of curvature in flagellar segments reveals the molecular mechanism enabling propulsive motility. Mechanistic understanding from could suggest engineering principles for nanoscale biomimetic systems.
History
DepositionJun 3, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70987.png

Downloads & links

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Map

FileDownload / File: emd_70987.map.gz / Format: CCP4 / Size: 479.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of the hook from Shewanella oneidensis. The above primary density map was upsampled from a pixel size of 1.1 A to 1.0 A and flipped to the correct handedness.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 501 pix.
= 501. Å		1 Å/pix.
x 501 pix.
= 501. Å		1 Å/pix.
x 501 pix.
= 501. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-0.1848857 - 12.984534
Average (Standard dev.)0.12355841 (±0.7596379)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions501501501
Spacing501501501
CellA=B=C: 501.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_70987_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_70987_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hook

EntireName: Hook
Components
  • Complex: Hook

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Supramolecule #1: Hook

SupramoleculeName: Hook / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)

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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: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 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: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 14363
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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