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- EMDB-75270: Native flagellar filament from Leptospira biflexa -

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Basic information

Entry
Database: EMDB / ID: EMD-75270
TitleNative flagellar filament from Leptospira biflexa
Map data
Sample
  • Complex: native flagellar filament
    • Protein or peptide: x 10 types
  • Ligand: x 2 types
KeywordsBacterial Endo-flagellum / Filament / PROTEIN FIBRIL
Function / homology
Function and homology information


periplasmic flagellum / bacterial-type flagellum-dependent cell motility / outer membrane-bounded periplasmic space / structural molecule activity
Similarity search - Function
: / : / LIC_12936-like / Surface protein adhesin OmpL37 / Flagellar filament outer layer protein FlaA / Flagellar filament outer layer protein Flaa / : / : / FcpA / : ...: / : / LIC_12936-like / Surface protein adhesin OmpL37 / Flagellar filament outer layer protein FlaA / Flagellar filament outer layer protein Flaa / : / : / FcpA / : / FcpB / 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
Uncharacterized protein / Uncharacterized protein / Flagellar filament outer layer protein (Sheath protein) putative signal peptide / Uncharacterized protein / Uncharacterized protein / Flagellin / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesLeptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBrady MR / San Martin F / Sindelar CV / Buschiazzo A
Funding supportUruguay, 1 items
OrganizationGrant numberCountry
Agencia Nacional de Investigacion e Innovacion (ANII)Uruguay
CitationJournal: Nat Commun / Year: 2026
Title: Core-sheath coupling controls flagellar curvature and motility in Leptospira.
Authors: Fabiana San Martin / Megan R Brady / Lenka Fule / Lucienne Nouchikian / Azalia Rodriguez / Magalie Duchateau / Sonia Mondino / Nicole Larrieux / Elsio A Wunder / Albert I Ko / Martial Rey / ...Authors: Fabiana San Martin / Megan R Brady / Lenka Fule / Lucienne Nouchikian / Azalia Rodriguez / Magalie Duchateau / Sonia Mondino / Nicole Larrieux / Elsio A Wunder / Albert I Ko / Martial Rey / Julia Chamot-Rooke / Rosario Duran / Felipe Trajtenberg / Mathieu Picardeau / Charles V Sindelar / Alejandro Buschiazzo /
Abstract: Spirochaete pathogens are among the most invasive bacteria known, causing syphilis, Lyme disease, and leptospirosis. Their tissue penetration depends on periplasmic flagellar filaments that, unlike ...Spirochaete pathogens are among the most invasive bacteria known, causing syphilis, Lyme disease, and leptospirosis. Their tissue penetration depends on periplasmic flagellar filaments that, unlike other bacterial flagella, are encased in a spirochaete-specific multi-protein sheath and deform the cell body into motile waves. How these filaments achieve the mechanical properties needed for invasive motility has remained unclear. Here we determine complete atomic structures of the Leptospira endoflagellar filament, revealing an elaborate sheath of 9 to 12 distinct asymmetrically arranged proteins. We show that the flagellin variant forming the filament core determines sheath composition, producing curvatures ranging from ~3.5 µm to ~5.6 µm. The lower-curvature architecture, employed by pathogenic Leptospira interrogans, proves essential for motility in viscous environments and during infection. Thus, Leptospira achieves environment-specific motility through modular core-sheath coupling, linking atomic-scale structural plasticity to large-scale changes in swimming behaviour. Conservation of key sheath components suggests this mechanism may extend across spirochaetes.
History
DepositionJan 26, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75270.png

Downloads & links

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Map

FileDownload / File: emd_75270.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.07 Å/pix.
x 256 pix.
= 273.408 Å		1.07 Å/pix.
x 256 pix.
= 273.408 Å		1.07 Å/pix.
x 256 pix.
= 273.408 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.5057013 - 0.9938325
Average (Standard dev.)-0.000000000000247 (±0.06480876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.408 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_75270_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_75270_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : native flagellar filament

EntireName: native flagellar filament
Components
  • Complex: native flagellar filament
    • Protein or peptide: Flagellin
    • Protein or peptide: Flagellar Coiling Protein FcpA
    • Protein or peptide: Flagellar Coiling Protein FcpB
    • Protein or peptide: LEPBI_I1029 protein
    • Protein or peptide: Flagellar filament outer layer protein (Sheath protein) putative signal peptide
    • Protein or peptide: FlaA2 associated protein B0STF2
    • Protein or peptide: FlaA2-associated protein FlaAP
    • Protein or peptide: LEPBI_I3081 protein
    • Protein or peptide: LEPBI_I0662 protein
    • Protein or peptide: LEPBI_II0033 protein
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: native flagellar filament

SupramoleculeName: native flagellar filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 70 / Enantiomer: LEVO
Source (natural)Organism: Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (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: Flagellar Coiling Protein FcpA

MacromoleculeName: Flagellar Coiling Protein FcpA / type: protein_or_peptide / ID: 2 / Number of copies: 27 / Enantiomer: LEVO
Source (natural)Organism: Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (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: Flagellar Coiling Protein FcpB

MacromoleculeName: Flagellar Coiling Protein FcpB / type: protein_or_peptide / ID: 3 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (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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Macromolecule #4: LEPBI_I1029 protein

MacromoleculeName: LEPBI_I1029 protein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
Molecular weightTheoretical: 37.285012 KDa
SequenceString: MQWLWVISHT STQCLQNKRI WGILIFENKE NLNFINVALS NLAPSQEEAQ TTAQPGAETP PQDPSKKNLD FDYFKLLKAA NQSDFSGNM WYLQSNYVYG FRQLRQAQGE LKNIFEIVLQ KYIEDARALL EAAAPTIIRS NDSNAKALLR LGFRDLRSSE D LYTTGLNS ...String:
MQWLWVISHT STQCLQNKRI WGILIFENKE NLNFINVALS NLAPSQEEAQ TTAQPGAETP PQDPSKKNLD FDYFKLLKAA NQSDFSGNM WYLQSNYVYG FRQLRQAQGE LKNIFEIVLQ KYIEDARALL EAAAPTIIRS NDSNAKALLR LGFRDLRSSE D LYTTGLNS SPHQYRYKLT LYKEGILTLR RAKRFAILAM IYSKTPDEDK PEYQYRSNED LKEARNEEKQ RNYEKVRDTL IN FIENKRM ERTVVPPGNP DAKPLDLLEQ HDDNYGFITS KKLDLLLEAN AQIKETEGAR RESVPPTPKF DENGKAIYPE EKK K

UniProtKB: Uncharacterized protein

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Macromolecule #5: Flagellar filament outer layer protein (Sheath protein) putative ...

MacromoleculeName: Flagellar filament outer layer protein (Sheath protein) putative signal peptide
type: protein_or_peptide / ID: 5 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
Molecular weightTheoretical: 27.630594 KDa
SequenceString: MSFMGKLGMT KLLLGLFLSI GMLYAQADTG GQNTANTAND EDSPLRKIVL DDFEEAEDWR VKATTPLGET RTLKLVQRGL IKDVFDEKT VPEDGGDKIE KNHILGVKTH FAAKGLDRVE LYPPHEYIIK GKVRQISVWV LGRKYRHTLF AKFRDYKDVT H NIRLGRLD ...String:
MSFMGKLGMT KLLLGLFLSI GMLYAQADTG GQNTANTAND EDSPLRKIVL DDFEEAEDWR VKATTPLGET RTLKLVQRGL IKDVFDEKT VPEDGGDKIE KNHILGVKTH FAAKGLDRVE LYPPHEYIIK GKVRQISVWV LGRKYRHTLF AKFRDYKDVT H NIRLGRLD FFGWRKLTAT VPGFIPQSTR FALLDKNLHF VSLFVTSDVH EVAGDFYFYV DDLQVRTDRS EAKYPGSEIK DN W

UniProtKB: Flagellar filament outer layer protein (Sheath protein) putative signal peptide

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Macromolecule #6: FlaA2 associated protein B0STF2

MacromoleculeName: FlaA2 associated protein B0STF2 / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
Molecular weightTheoretical: 33.018371 KDa
SequenceString: MNKTIFALSF TLLSFALFAQ ESGNPQGTQV SAASSKDNRD LYPLSMYDAR IRLKNVTFVR RHADTGKGEF LDVQVEIESR VPEDHEYSI FVLAGFEGDR VNKDERKLVP YPAWRKADPE KDERTLYFSN IMPTPFTAKE IWGEETYAKK KEEMEKRHYA G FEAAMPEP ...String:
MNKTIFALSF TLLSFALFAQ ESGNPQGTQV SAASSKDNRD LYPLSMYDAR IRLKNVTFVR RHADTGKGEF LDVQVEIESR VPEDHEYSI FVLAGFEGDR VNKDERKLVP YPAWRKADPE KDERTLYFSN IMPTPFTAKE IWGEETYAKK KEEMEKRHYA G FEAAMPEP TFTEVVDYLC KNNAKALPFT LFGETGPSKE KQVIYNYVGQ TADEKKRQVH ETLPKHTYTI YNNKYKTTIT SH HYTQYRP NFLSFNKVAI LVFDTKKPTN SLLFRKFIDI SDLKITY

UniProtKB: Uncharacterized protein

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Macromolecule #7: FlaA2-associated protein FlaAP

MacromoleculeName: FlaA2-associated protein FlaAP / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
Molecular weightTheoretical: 43.060012 KDa
SequenceString: MKQSLLILMM SLVMQAPMFA ESVSSKSYQK RIELLTYLRE LEPIVKNFRG EDPEGKPSEL NAPEGKEGFR MKKYLEAKRI YQEGLQYHF EGNFSSAFQR FLECQLAIEK MTEELSQLYI LRAEEMMKTA MERKNPNNPM DKALLDISIE YGKGSYFRQD V MDLPREAP ...String:
MKQSLLILMM SLVMQAPMFA ESVSSKSYQK RIELLTYLRE LEPIVKNFRG EDPEGKPSEL NAPEGKEGFR MKKYLEAKRI YQEGLQYHF EGNFSSAFQR FLECQLAIEK MTEELSQLYI LRAEEMMKTA MERKNPNNPM DKALLDISIE YGKGSYFRQD V MDLPREAP YQRRMYDPKE AHYSYNKYDI EKNMELGYKH LGLAKEARAN ALKVERNLEK HQKLQPSHRK YRIELYFGAI NL ARDSKAN AVNIYKLKYP YDNYYLNNSQ AKTEASKDET GASVEGQPVK IDGVTYDFTK NPYIKYDNRL QAMFDVRVPE EYR VDHADV RGRVYELDSN NMVFMKYDQE RKKALNVPPK PAQGSTTTPQ Q

UniProtKB: Uncharacterized protein

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Macromolecule #8: LEPBI_I3081 protein

MacromoleculeName: LEPBI_I3081 protein / type: protein_or_peptide / ID: 8 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
Molecular weightTheoretical: 27.089711 KDa
SequenceString: MRTSFVLIFT FLFTVGLFAA DEKNESVSQS DATKLNPDGS IALIPYNAKQ QQKIERIGKE VDDYHAMINE KVKFLSFEKK IKDSRYGQV TSAREIHLPY EPSYVMHSRF VMKLKGGGGA EGGGFSLDEI SFWSRKSLTE KGKDPVTTYR ELKNNTTGGV K GLVLSVRT ...String:
MRTSFVLIFT FLFTVGLFAA DEKNESVSQS DATKLNPDGS IALIPYNAKQ QQKIERIGKE VDDYHAMINE KVKFLSFEKK IKDSRYGQV TSAREIHLPY EPSYVMHSRF VMKLKGGGGA EGGGFSLDEI SFWSRKSLTE KGKDPVTTYR ELKNNTTGGV K GLVLSVRT VTNADDNTLN FELEKIQSPW ERLRLATAYR DRLREVARTI DRYIQAKGNL ETKMISDTVM EVSVSGDFEE P

UniProtKB: Uncharacterized protein

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Macromolecule #9: LEPBI_I0662 protein

MacromoleculeName: LEPBI_I0662 protein / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
Molecular weightTheoretical: 31.206863 KDa
SequenceString: MMLRFSILLC YLLGMTALFA EKPASATLKE RESQKQIDLQ RKNGFGDNEI DTLHANIIGN LRKIKKLQDL GVDKTAAQYL AQTPQEHKE LYKKDKDGKP YLEIKLPQGQ SYIDYPSVFL YDGIAYIYPK EDYSDLDKII LSFRRVNADG TIHVKEMRRL I NPTPKSEG ...String:
MMLRFSILLC YLLGMTALFA EKPASATLKE RESQKQIDLQ RKNGFGDNEI DTLHANIIGN LRKIKKLQDL GVDKTAAQYL AQTPQEHKE LYKKDKDGKP YLEIKLPQGQ SYIDYPSVFL YDGIAYIYPK EDYSDLDKII LSFRRVNADG TIHVKEMRRL I NPTPKSEG TEKDEKGEAR LDTNSDIRLE YFRSLTSDTI WPNDPVQPAE ADIAMVLNDE KDPLPYDKQK HIMMSYKKML RK IAKQTAF KLRSVELDQK QMITKILDYN TN

UniProtKB: Uncharacterized protein

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Macromolecule #10: LEPBI_II0033 protein

MacromoleculeName: LEPBI_II0033 protein / type: protein_or_peptide / ID: 10 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
Molecular weightTheoretical: 20.826744 KDa
SequenceString:
MELSKKSLLF ILMFSLAVFS ISAQDTKPQS TSTDVTQENH DAKEGQDKEL FEYYYKTRPE NLPPNKAKLE YNLIKTLKKE IMSRDYSKE SAESIKKIDA TNIQYERVYR DSKWLRGFMT QNTHLNYMEF MYVVKYDKYM CFVTFDVNPE NYLQQSRQSH L VFSGKDKF EITIPKP

UniProtKB: Uncharacterized protein

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Macromolecule #11: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 11 / Number of copies: 10 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #12: water

MacromoleculeName: water / type: ligand / ID: 12 / Number of copies: 20 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 25.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Sheathless straight flagellar filament 3D map
Details: filtered to 20 angstroems resolution
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1)
Details: Further Density Modification with Phenix Resolve increased resolution to 3.2 angstroems and better resolved features in the cryoEM map
Number images used: 176558
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: projection matching
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: integrative model
Details: we used comparative proteomics (wt and mutants) plus cross-linked+MS data; AlphaFold-redicted Initial models; and crystallographic structures
Detailsiteration between real space refinement with Phenix.real_space_refine, and Servalcat (reciprocal space)
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-10lm:
Native flagellar filament from Leptospira biflexa

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