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- PDB-9x7l: core filament of the spirochete periplasmic flagella of Leptospir... -

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Basic information

Entry
Database: PDB / ID: 9x7l
Titlecore filament of the spirochete periplasmic flagella of Leptospira biflexa from the flaA2-complemented stain
ComponentsFlagellin
KeywordsMOTOR PROTEIN / Filament / Flagellar motor
Function / homologyperiplasmic flagellum / 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 / structural molecule activity / Flagellin
Function and homology information
Biological speciesLeptospira biflexa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsKawamoto, A. / Nakamura, S. / Koizumi, N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K02274 Japan
Japan Science and TechnologyJPMJPR21E5 Japan
CitationJournal: EMBO J / Year: 2026
Title: Asymmetric sheath coordination controls flagellar architecture and function in Leptospira spirochete.
Authors: Akihiro Kawamoto / Toshiki Kuribayashi / Masatomo Morita / Shuichi Nakamura / Nobuo Koizumi /
Abstract: Bacterial flagella are essential for motility, but their structure and how they generate movement vary greatly. Most motile bacteria use external helical flagella, whereas spirochetes have ...Bacterial flagella are essential for motility, but their structure and how they generate movement vary greatly. Most motile bacteria use external helical flagella, whereas spirochetes have periplasmic flagella (PFs) that distort the cell body to drive forward movement. Here, we generated sheath protein knockout mutants and used high-resolution cryo-electron microscopy to elucidate the mechanisms underlying PF assembly, curvature, and rigidity in Leptospira biflexa. The PF consists of a FlaB1-based core filament surrounded asymmetrically by sheath proteins. Weak but essential binding of FlaA2 to the core enables asymmetric localization of the coiling protein FcpA. FcpA alone can induce curvature, whereas FcpB acts as a structural wedge that reinforces PF rigidity and enables efficient swimming in liquid. Specific glycosylation of FlaB1 mediates sheath-core interactions and may guide the assembly of sheath components. We propose that sheath proteins interact transiently with the core and may be anchored to the outer membrane, allowing core rotation beneath a static sheath. These findings reveal how cooperative interactions among sheath components confer structural and mechanical specialization to spirochete flagella.
History
DepositionOct 17, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
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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


Theoretical massNumber of molelcules
Total (without water)343,96111
Polymers343,96111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Flagellin


Mass: 31269.217 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Leptospira biflexa (bacteria) / References: UniProt: B0SSZ5
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: core filament of the spirochete periplasmic flagella from the flaA2-complemented strain
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Leptospira biflexa (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.782 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14160
Details: To analyze the asymmetric structure, data were collected under two conditions: with the stage tilted 30 degree, and without tilting
EM imaging opticsEnergyfilter slit width: 20 eV
Spherical aberration corrector: Microscope was modified with a Cs corrector
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2SerialEMimage acquisition
4cryoSPARC4.2.1CTF correction
7Coot0.9.8.7model fitting
9PHENIX1.21.1_5286model refinement
10cryoSPARC4.2.1initial Euler assignment
11cryoSPARC4.2.1final Euler assignment
12cryoSPARC4.2.1classification
13cryoSPARC4.2.13D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 457214 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 9LRZ

9lrz


Accession code: 9LRZ / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 103.24 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003124112
ELECTRON MICROSCOPYf_angle_d0.554432406
ELECTRON MICROSCOPYf_chiral_restr0.03743696
ELECTRON MICROSCOPYf_plane_restr0.00274334
ELECTRON MICROSCOPYf_dihedral_angle_d6.68873431

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