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- PDB-9lry: Straight and symmetrical filament of the spirochete periplasmic f... -

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Basic information

Entry
Database: PDB / ID: 9lry
TitleStraight and symmetrical filament of the spirochete periplasmic flagella of Leptospira biflexa
Components
  • (Bacterial flagellar sheath protein) x 2
  • Flagellin
KeywordsMOTOR PROTEIN / Filament / Flagellar motor
Function / homology: / : / Uncharacterized protein
Function and homology information
Biological speciesLeptospira biflexa (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.3 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
DepositionFeb 2, 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: FSC / Data content type: FSC / 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: 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
C: Bacterial flagellar sheath protein
B: Bacterial flagellar sheath protein


Theoretical massNumber of molelcules
Total (without water)98,8583
Polymers98,8583
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.: 1 / Source method: isolated from a natural source / Source: (natural) Leptospira biflexa (bacteria) / References: UniProt: A0AAQ2CUK9
#2: Protein Bacterial flagellar sheath protein


Mass: 31565.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leptospira biflexa (bacteria) / References: UniProt: B0SR03
#3: Protein Bacterial flagellar sheath protein


Mass: 35876.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leptospira biflexa (bacteria) / References: UniProt: A0AAQ2CSE7
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Straight and symmetrical filament of the spirochete periplasmic flagella
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
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: 84.18 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: 2318
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
2EPUimage acquisition
4GctfCTF correction
7Cootmodel fitting
9RELION3.1.3initial Euler assignment
10RELION3.1.3final Euler assignment
11RELION3.1.3classification
12RELION3.1.33D reconstruction
13PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: 65.425 ° / Axial rise/subunit: 4.836 Å / Axial symmetry: C1
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138670 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL
Atomic model buildingB value: 45.5861 / Protocol: FLEXIBLE FIT / Space: REAL
RefinementHighest resolution: 2.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026319
ELECTRON MICROSCOPYf_angle_d0.438496
ELECTRON MICROSCOPYf_dihedral_angle_d4.682839
ELECTRON MICROSCOPYf_chiral_restr0.037910
ELECTRON MICROSCOPYf_plane_restr0.0031108

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