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- PDB-9oxk: CryoEM structure of FlaB filament from Shewanella oneidensis -

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Basic information

Entry
Database: PDB / ID: 9oxk
TitleCryoEM structure of FlaB filament from Shewanella oneidensis
ComponentsFlagellin
KeywordsSTRUCTURAL PROTEIN / FlaB filament
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
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 speciesShewanella oneidensis MR-1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsQing, L. / Fan, H.C. / Liu, Y. / Miller, J.F. / Huang, Y. / Zhou, Z.H.
Funding support United States, 4items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellin
B: Flagellin
C: Flagellin
D: Flagellin
E: Flagellin
F: Flagellin
G: Flagellin
H: Flagellin
I: Flagellin
J: Flagellin
K: Flagellin
L: Flagellin
M: Flagellin
N: Flagellin
O: Flagellin
P: Flagellin
Q: Flagellin
R: Flagellin
S: Flagellin
T: Flagellin
U: Flagellin
V: Flagellin
W: Flagellin
X: Flagellin
Y: Flagellin
Z: Flagellin
a: Flagellin
b: Flagellin
c: Flagellin
d: Flagellin
e: Flagellin
f: Flagellin


Theoretical massNumber of molelcules
Total (without water)907,66932
Polymers907,66932
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Flagellin


Mass: 28364.670 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Source: (natural) Shewanella oneidensis MR-1 (bacteria) / References: UniProt: Q8ECA6
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: FlaB filament / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: RELION / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 463640 / Symmetry type: POINT
RefinementHighest resolution: 2.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00763456
ELECTRON MICROSCOPYf_angle_d0.72685504
ELECTRON MICROSCOPYf_dihedral_angle_d4.5538992
ELECTRON MICROSCOPYf_chiral_restr0.04610496
ELECTRON MICROSCOPYf_plane_restr0.00511392

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