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- EMDB-66649: sheathed filament of the spirochete periplasmic flagella of Lepto... -

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Basic information

Entry
Database: EMDB / ID: EMD-66649
Titlesheathed filament of the spirochete periplasmic flagella of Leptospira biflexa wild type
Map data
Sample
  • Complex: sheathed filament of the spirochete periplasmic flagella from wild type
    • Protein or peptide: Flagellin
    • Protein or peptide: Bacterial flagellar sheath protein
    • Protein or peptide: Bacterial flagellar sheath protein
KeywordsFilament / Flagellar motor / MOTOR PROTEIN
Function / homology
Function and homology information


periplasmic flagellum / structural molecule activity
Similarity search - Function
: / FcpB / : / : / FcpA / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.24 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
DepositionOct 18, 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_66649.png

Downloads & links

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Map

FileDownload / File: emd_66649.map.gz / Format: CCP4 / Size: 512 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 512 pix.
= 578.56 Å		1.13 Å/pix.
x 512 pix.
= 578.56 Å		1.13 Å/pix.
x 512 pix.
= 578.56 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: 0.273
Minimum - Maximum-2.6968594 - 3.8391457
Average (Standard dev.)0.0026715 (±0.071264856)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 578.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66649_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_66649_additional_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66649_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66649_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : sheathed filament of the spirochete periplasmic flagella from wil...

EntireName: sheathed filament of the spirochete periplasmic flagella from wild type
Components
  • Complex: sheathed filament of the spirochete periplasmic flagella from wild type
    • Protein or peptide: Flagellin
    • Protein or peptide: Bacterial flagellar sheath protein
    • Protein or peptide: Bacterial flagellar sheath protein

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Supramolecule #1: sheathed filament of the spirochete periplasmic flagella from wil...

SupramoleculeName: sheathed filament of the spirochete periplasmic flagella from wild type
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: 11 / 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: Flagellin

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Macromolecule #2: Bacterial flagellar sheath protein

MacromoleculeName: Bacterial flagellar sheath protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / 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: Uncharacterized protein

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Macromolecule #3: Bacterial flagellar sheath protein

MacromoleculeName: Bacterial flagellar sheath protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Leptospira biflexa (bacteria)
Molecular weightTheoretical: 31.565652 KDa
SequenceString: MKIKLILPIL LLSIGVFAQT GSSETGSTSA GIDPSQSGKS MADTEKELDD NISEVNKRLR LHTVLFKMKV RTLPHKTVLY KGKPSADGE RCEAADKQEA QDNTCLHLEV FDFVGSEDGK SSKNLGAKFK KMELFFEGSN NADPDPRKEQ PRNLTKIRTY I YQNNFLLE ...String:
MKIKLILPIL LLSIGVFAQT GSSETGSTSA GIDPSQSGKS MADTEKELDD NISEVNKRLR LHTVLFKMKV RTLPHKTVLY KGKPSADGE RCEAADKQEA QDNTCLHLEV FDFVGSEDGK SSKNLGAKFK KMELFFEGSN NADPDPRKEQ PRNLTKIRTY I YQNNFLLE DKVISVIADV APNGEPAHND KIELFYQHDD YPVWGTPETP SEKGVGKYIL SNVENTKSNP IRNNFKKQFY FK NLDYFDK LFTKIFDYND RDSNKHYKKN VEALKGSLKY

UniProtKB: Uncharacterized protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle 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: 2614 / Average exposure time: 83.81 sec. / Average electron dose: 50.0 e/Å2
Details: To analyze the asymmetric structure, data were collected under two conditions: with the stage tilted 30 degree, and without tilting
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

CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 163413
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.2.1)

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Atomic model buiding 1

Initial modelPDB ID:

9lrz


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9x80:
sheathed filament of the spirochete periplasmic flagella of Leptospira biflexa wild type

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