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- EMDB-63349: Straight and symmetrical filament of the spirochete periplasmic f... -

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Basic information

Entry
Database: EMDB / ID: EMD-63349
TitleStraight and symmetrical filament of the spirochete periplasmic flagella of Leptospira biflexa deleted fcpB strain
Map data
Sample
  • Complex: Straight and symmetrical filament of the spirochete periplasmic flagella from deleted fcpB strain
    • Protein or peptide: Flagellin
    • Protein or peptide: Bacterial flagellar sheath protein
KeywordsFilament / Flagellar motor / MOTOR PROTEIN
Function / homology: / :
Function and homology information
Biological speciesLeptospira biflexa (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsKawamoto A / Nakamura S / Koizumi N
Funding support Japan, 2 items
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
DepositionFeb 2, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63349.png

Downloads & links

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Map

FileDownload / File: emd_63349.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 360 pix.
= 406.8 Å		1.13 Å/pix.
x 360 pix.
= 406.8 Å		1.13 Å/pix.
x 360 pix.
= 406.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0415
Minimum - Maximum-0.33139265 - 0.46499664
Average (Standard dev.)0.000031291955 (±0.004282149)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 406.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_63349_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #1

Fileemd_63349_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63349_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Straight and symmetrical filament of the spirochete periplasmic f...

EntireName: Straight and symmetrical filament of the spirochete periplasmic flagella from deleted fcpB strain
Components
  • Complex: Straight and symmetrical filament of the spirochete periplasmic flagella from deleted fcpB strain
    • Protein or peptide: Flagellin
    • Protein or peptide: Bacterial flagellar sheath protein

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Supramolecule #1: Straight and symmetrical filament of the spirochete periplasmic f...

SupramoleculeName: Straight and symmetrical filament of the spirochete periplasmic flagella from deleted fcpB strain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Leptospira biflexa (bacteria)

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Leptospira biflexa (bacteria)
Molecular weightTheoretical: 31.415635 KDa
SequenceString: MIINHNVSAI FAHRTLKSND ANLSKDIEKL SSGMRINKAG DDASGLAVSE KMRTQIAGLR RAEQNTEDGM SLIQTAEGYL QETHEIVQR VRVLAVQAAN GIYSEEDRQQ IQVEVSQLVD EIDRIASQAE FNKMKLLTGA FARLNPTASM WFHIGANMHQ R ERVYIETM ...String:
MIINHNVSAI FAHRTLKSND ANLSKDIEKL SSGMRINKAG DDASGLAVSE KMRTQIAGLR RAEQNTEDGM SLIQTAEGYL QETHEIVQR VRVLAVQAAN GIYSEEDRQQ IQVEVSQLVD EIDRIASQAE FNKMKLLTGA FARLNPTASM WFHIGANMHQ R ERVYIETM NTAALGLRNP TVLTFISLST AGKANSVIGL CDDALRVISK QRADLGAYYN RMEHAAKGLM NAYENTQASE SR IRDTDMA EQMTSFTRYQ ILTQAATSML AQANMKSQSV MRLLQ

UniProtKB: UNIPROTKB: A0AAQ2CUK9

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Macromolecule #2: Bacterial flagellar sheath protein

MacromoleculeName: Bacterial flagellar sheath protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Leptospira biflexa (bacteria)
Molecular weightTheoretical: 35.876797 KDa
SequenceString: MKIIKYLLIL QLVSGFSVLF AQTQPANAQE SQAAKDQVDE LLKGELVPEN DDAELTEDQK KKKKEIMEQE SLWKNPDFKG YNKTFQELH QLSKTFANNQ FRLALSNYQS GVNTIMKNRD WVEQYRKEEA EKKRLDEKWY WQKVDRKARE ERVVYREKMK A KQDALNYF ...String:
MKIIKYLLIL QLVSGFSVLF AQTQPANAQE SQAAKDQVDE LLKGELVPEN DDAELTEDQK KKKKEIMEQE SLWKNPDFKG YNKTFQELH QLSKTFANNQ FRLALSNYQS GVNTIMKNRD WVEQYRKEEA EKKRLDEKWY WQKVDRKARE ERVVYREKMK A KQDALNYF SKAINHLDEI KNPDLRERPE FKRLLSDVYR SWIMAEYDLQ NLPQTIPILE LYIEIDDNEK EYPAHKYLAS AY SFEENMI KKTKGPDDML FKYRYKKNVH LLRATELKYG KDSPEYKHIV NVINRDEVIS VAQ

UniProtKB: UNIPROTKB: A0AAQ2CSE7

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 1632 / Average exposure time: 83.81 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.81 Å
Applied symmetry - Helical parameters - Δ&Phi: 65.439 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 203738
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 50.5914
Output model

PDB-9ls0:
Straight and symmetrical filament of the spirochete periplasmic flagella of Leptospira biflexa deleted fcpB strain

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