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- PDB-9x80: sheathed filament of the spirochete periplasmic flagella of Lepto... -

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Basic information

Entry
Database: PDB / ID: 9x80
Titlesheathed filament of the spirochete periplasmic flagella of Leptospira biflexa wild type
Components
  • (Bacterial flagellar sheath protein) x 2
  • Flagellin
KeywordsMOTOR PROTEIN / Filament / Flagellar motor
Function / homology
Function and homology information


periplasmic flagellum / structural molecule activity
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
Flagellin / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesLeptospira biflexa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 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: To Be Published
Title: Cooperativity of sheath proteins in the flagellar assembly of Leptospira spirochete
Authors: Kawamoto, A. / Kuribayashi, T. / Morita, M. / Nakamura, S. / Koizumi, N.
History
DepositionOct 18, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: 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
D: Flagellin
G: Flagellin
J: Flagellin
K: Bacterial flagellar sheath protein
L: Bacterial flagellar sheath protein
M: Flagellin
N: Bacterial flagellar sheath protein
O: Bacterial flagellar sheath protein
P: Flagellin
Q: Bacterial flagellar sheath protein
R: Bacterial flagellar sheath protein
S: Flagellin
V: Flagellin
Y: Flagellin
Z: Bacterial flagellar sheath protein
a: Bacterial flagellar sheath protein
b: Flagellin
c: Bacterial flagellar sheath protein
d: Bacterial flagellar sheath protein
e: Flagellin
f: Bacterial flagellar sheath protein
g: Bacterial flagellar sheath protein


Theoretical massNumber of molelcules
Total (without water)750,22723
Polymers750,22723
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: 31415.635 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Leptospira biflexa (bacteria) / References: UniProt: B0SQZ5
#2: Protein
Bacterial flagellar sheath protein


Mass: 35876.797 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Leptospira biflexa (bacteria) / References: UniProt: B0STJ8
#3: Protein
Bacterial flagellar sheath protein


Mass: 31565.652 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Leptospira biflexa (bacteria) / References: UniProt: B0SR03
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: sheathed filament of the spirochete periplasmic flagella from wild type
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: 59000 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: 83.81 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2614
Details: To analyze the asymmetric structure, data were collected under two conditions: with the stage tilted 30 degree, and without tilting
EM imaging opticsSpherical aberration corrector: Microscope was modified with a Cs corrector
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2EPUimage 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: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 163413 / 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: 97.41 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001448854
ELECTRON MICROSCOPYf_angle_d0.330565696
ELECTRON MICROSCOPYf_chiral_restr0.03417150
ELECTRON MICROSCOPYf_plane_restr0.00228583
ELECTRON MICROSCOPYf_dihedral_angle_d9.966918792

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