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- EMDB-75269: Native flagellar filament from Leptospira interrogans flaB1- KO m... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-75269
TitleNative flagellar filament from Leptospira interrogans flaB1- KO mutant strain
Map data
Sample
  • Complex: native endoflagellar filament
    • Protein or peptide: x 11 types
  • Ligand: x 2 types
KeywordsBacterial Endo-flagellum / Filament / PROTEIN FIBRIL
Function / homology
Function and homology information


: / : / : / : / : / : / : / Uncharacterized protein / : / : / :
Similarity search - Component
Biological speciesLeptospira interrogans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 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_75269.png

Downloads & links

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Map

FileDownload / File: emd_75269.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: 0.04
Minimum - Maximum-0.226623 - 0.40544546
Average (Standard dev.)-0.000000000000015 (±0.037477974)
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_75269_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_75269_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 endoflagellar filament

EntireName: native endoflagellar filament
Components
  • Complex: native endoflagellar filament
    • Protein or peptide: Flagellin
    • Protein or peptide: Flagellar Coiling Protein FcpA
    • Protein or peptide: Flagellar Coiling Protein FcpB
    • Protein or peptide: Flagellar filament sheath protein
    • Protein or peptide: AraC family transcriptional regulator
    • Protein or peptide: Flagellar filament outer layer protein FlaA
    • Protein or peptide: LIC_12075 protein
    • Protein or peptide: FlaA2-associated protein FlaAP
    • Protein or peptide: DUF4468 domain-containing protein
    • Protein or peptide: LIC_13212 protein
    • Protein or peptide: Lipoprotein
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: native endoflagellar filament

SupramoleculeName: native endoflagellar filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Leptospira interrogans (bacteria) / Strain: flaB1- KO mutant

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 64 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans (bacteria) / Strain: flaB1- KO mutant
Molecular weightTheoretical: 31.507916 KDa
SequenceString: MIINHNISAI FAHRTLKFNS ESMGKDIEKL SSGMRINRAG DDASGLAVSE KMRTQILGLR RAEMNTEDGM SLIQTTEGYL QETHEIVQR IRVLAVQAAN GIYTEEDRQQ IQVEVSQLVD EIDRIASQAE FNKMKLLTGA FARLNPTASM WFHIGANMHQ R ERVYIETM ...String:
MIINHNISAI FAHRTLKFNS ESMGKDIEKL SSGMRINRAG DDASGLAVSE KMRTQILGLR RAEMNTEDGM SLIQTTEGYL QETHEIVQR IRVLAVQAAN GIYTEEDRQQ IQVEVSQLVD EIDRIASQAE FNKMKLLTGA FARLNPTASM WFHIGANMHQ R ERVYIETM NTAALGLRNP TVLTFISLST AGKANSVIGL ADDALRSISK QRADLGAYYN RLEHAAKGLM NAYENIQAAE SR IRDTDMA EQMTSFTRYQ ILTQAATAML AQANMKPQTV LQLLK

UniProtKB: UNIPROTKB: Q72S55

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Macromolecule #2: Flagellar Coiling Protein FcpA

MacromoleculeName: Flagellar Coiling Protein FcpA / type: protein_or_peptide / ID: 2 / Number of copies: 25 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans (bacteria) / Strain: flaB1- KO mutant
Molecular weightTheoretical: 36.270336 KDa
SequenceString: MSIMKVMKSI FILLAVLGLN LSVLAQQNNQ GGNQQANESV EKIDELLKGE LVPEDDDKNL TEEQKRRKKA IQEQEALWKN PDFKGYDKN FQELHQLSKA FANNKFRLAL SNYQSGVNTI LKMREAIEQY RKEEAEKKRL DEKWYWQKVD RKAREDRVVS R DKLVAKQQ ...String:
MSIMKVMKSI FILLAVLGLN LSVLAQQNNQ GGNQQANESV EKIDELLKGE LVPEDDDKNL TEEQKRRKKA IQEQEALWKN PDFKGYDKN FQELHQLSKA FANNKFRLAL SNYQSGVNTI LKMREAIEQY RKEEAEKKRL DEKWYWQKVD RKAREDRVVS R DKLVAKQQ ALNYFTKAIN HLDEIKNPDL RERPEFKRLL SDTYRSWILT EYDLQNLPQC IPILELYIEI DENEKEYPAH KY LASCYAF EENMIKKNGG ASEDQMFKYR YKKNVHLLRA TELKYGKDSP EYKHIVNLVN KDEVISVRP

UniProtKB: UNIPROTKB: Q72MM7

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Macromolecule #3: Flagellar Coiling Protein FcpB

MacromoleculeName: Flagellar Coiling Protein FcpB / type: protein_or_peptide / ID: 3 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans (bacteria) / Strain: flaB1- KO mutant
Molecular weightTheoretical: 32.067277 KDa
SequenceString: MKLQKLFLAV LIAISTAVFS QQNSGSDQKS QPSSAQLGQS ILETERKLDE KIFELNQRLT RHTVLMKMKV RVLPFRTVLF KGKANNDEC TPAINQEDPA NNCIRVEVYD FIRDEERGLN KNVQGALAKY MEIYFEGQNS NDPEPRTEPP RNINKLKSKI Y KNNMVLED ...String:
MKLQKLFLAV LIAISTAVFS QQNSGSDQKS QPSSAQLGQS ILETERKLDE KIFELNQRLT RHTVLMKMKV RVLPFRTVLF KGKANNDEC TPAINQEDPA NNCIRVEVYD FIRDEERGLN KNVQGALAKY MEIYFEGQNS NDPEPRTEPP RNINKLKSKI Y KNNMVLED KIISEVMDRG PNTQPSHNDK VEVFFQKDNY PEYGRPETPA EKGVGKYILA GVENTKTHPI RNSFKKEFYI KH LDQFDRL FTKIFDYNDQ LGNENYKENV DALKDSLRY

UniProtKB: Uncharacterized protein

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Macromolecule #4: Flagellar filament sheath protein

MacromoleculeName: Flagellar filament sheath protein / type: protein_or_peptide / ID: 4 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans (bacteria) / Strain: flaB1- KO mutant
Molecular weightTheoretical: 34.930551 KDa
SequenceString: MRRFMNSFKI TAALTTILGG VILLGIVNGQ NIIKGKRGID TATGIDVSGL ELRSITVESW DNPAPSAPYG WEVTTDKDTQ QPQGGQQQA YQATAQNAQA LREVKLISGK PGDIKNVDAG TAKVLGVKFQ FTYPGENAVT IRPPRIPEYE ILRTKAYLDA N NQKKVSKI ...String:
MRRFMNSFKI TAALTTILGG VILLGIVNGQ NIIKGKRGID TATGIDVSGL ELRSITVESW DNPAPSAPYG WEVTTDKDTQ QPQGGQQQA YQATAQNAQA LREVKLISGK PGDIKNVDAG TAKVLGVKFQ FTYPGENAVT IRPPRIPEYE ILRTKAYLDA N NQKKVSKI YGVEFPGVSK AMSVWVCGRG NEYNLEGWIE DWKGDTHILQ FGSLDFIGWR PLTVYIPQGV PQDVNSYPQV KT IVFKQFK VRSRPDTSGE TVYLFFDELR VLSDVFEVHF DGASIDFDDE DCRSKHKLDK MLKTKVEKEC GGGGAAGK

UniProtKB: UNIPROTKB: Q72U74

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Macromolecule #5: AraC family transcriptional regulator

MacromoleculeName: AraC family transcriptional regulator / type: protein_or_peptide / ID: 5 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans (bacteria) / Strain: flaB1- KO mutant
Molecular weightTheoretical: 37.561961 KDa
SequenceString: MLSKIQTILI VIILVFGELL WAVSPDQINL GILIGENKTN LKFINICVSN LAPILEPTNS DTSPPNNTKV EAGNTTTEVG DKVELFKKL GALPSYISLK KANQFDFNGN MLYFQSNYSL SFKNLRGAQG EMKDLYQATH EQYLQNSRIL LEYASPLIVR S NDKIAQHL ...String:
MLSKIQTILI VIILVFGELL WAVSPDQINL GILIGENKTN LKFINICVSN LAPILEPTNS DTSPPNNTKV EAGNTTTEVG DKVELFKKL GALPSYISLK KANQFDFNGN MLYFQSNYSL SFKNLRGAQG EMKDLYQATH EQYLQNSRIL LEYASPLIVR S NDKIAQHL LRLGFRDLKS SEDHFTIAYN SAPYQFRYKL LLHGEGIKIA RRARKFALLA MIASKTPTED KPEYQFVNLD DM RAAVEKE TITDYEKVRN TLINYIDNDL LQRKIVPPGE AKDKPIDILE IHDDNYGIIT SGRISMMDMS NEEIKTSDAI QKE TLPPIP TKTQN

UniProtKB: UNIPROTKB: A0AAV9G275

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Macromolecule #6: Flagellar filament outer layer protein FlaA

MacromoleculeName: Flagellar filament outer layer protein FlaA / type: protein_or_peptide / ID: 6 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans (bacteria) / Strain: flaB1- KO mutant
Molecular weightTheoretical: 27.218984 KDa
SequenceString: MRKKIILLAG LLCILAVPGV YSQQTGNNQA GGNQQTGANP DPLEKLILEN FEEAEDWRAK STTPLGETKV LKMVQRGLIR DVFDENTVP DNGGDQIEKN HILGVKTNYT VRGFDRVEVF PPHEYVVKGK ARQLSIWALG RKFRHTLFAK LRDYRGNTHN I RLGRLDYF ...String:
MRKKIILLAG LLCILAVPGV YSQQTGNNQA GGNQQTGANP DPLEKLILEN FEEAEDWRAK STTPLGETKV LKMVQRGLIR DVFDENTVP DNGGDQIEKN HILGVKTNYT VRGFDRVEVF PPHEYVVKGK ARQLSIWALG RKFRHTLFAK LRDYRGNTHN I RLGRLDYF GWRKLTATIP GFVPQSTRFA LLDKNLHFVS LFVVSDVHEV GGQFYFYVDD LEVRADKSDA KYPGSEIKDN W

UniProtKB: UNIPROTKB: A0AAV9FYL3

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Macromolecule #7: LIC_12075 protein

MacromoleculeName: LIC_12075 protein / type: protein_or_peptide / ID: 7 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans (bacteria) / Strain: flaB1- KO mutant
Molecular weightTheoretical: 33.009527 KDa
SequenceString: MKSFLRISVC LLLLFVGHTT FGQNAEKTDP NKKDGGTEYY PLAYYDERLS VKNISFFRRH SDNGKGEFLD VMVEMENRSF DPAKFSIYI LAINETTSIN PEKRDLVPFP KWRGFDLENN TFVINFQNLM PQKLEPKAVW GEEKYNKAKK DYDDRIARGE I VRMSNPSL ...String:
MKSFLRISVC LLLLFVGHTT FGQNAEKTDP NKKDGGTEYY PLAYYDERLS VKNISFFRRH SDNGKGEFLD VMVEMENRSF DPAKFSIYI LAINETTSIN PEKRDLVPFP KWRGFDLENN TFVINFQNLM PQKLEPKAVW GEEKYNKAKK DYDDRIARGE I VRMSNPSL TETVTYLTNH SENALEFTIF GEQGPKKDQV LISNFVDQTE EERKKQAHES LSKHTYTIYS AKYKTTLMSH HY TEYRPGY VTYNKVVVLI FNPLKEKNKL VYRRFIDIGG IKLLN

UniProtKB: UNIPROTKB: Q72QN8

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Macromolecule #8: FlaA2-associated protein FlaAP

MacromoleculeName: FlaA2-associated protein FlaAP / type: protein_or_peptide / ID: 8 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans (bacteria) / Strain: flaB1- KO mutant
Molecular weightTheoretical: 43.318246 KDa
SequenceString: MKRLILISIL ISILPVSVFG EAVSSKAYKK RVELLLYLRA IEPIVRNYKG EVPGGQNQQN TGATAANNQQ TGGAPEQDGD RVKKYKELK RLYQEGLQYF FENNHVNAYR RFLEAQLGTE MLLEELSQFY VERTEEILKS AIEKKNPNNP EDRNLVDIAI E WSKNSFIV ...String:
MKRLILISIL ISILPVSVFG EAVSSKAYKK RVELLLYLRA IEPIVRNYKG EVPGGQNQQN TGATAANNQQ TGGAPEQDGD RVKKYKELK RLYQEGLQYF FENNHVNAYR RFLEAQLGTE MLLEELSQFY VERTEEILKS AIEKKNPNNP EDRNLVDIAI E WSKNSFIV RDMTANREAP LTRRMYNPRD FHYVTNKYAI EKNMEMGYKF LGLAKETRNN ALKIEKHLEK HQKLQPSHRK HR IEHYIAA IQLCRDARAN AINIFKLKYP YDNYYLFKSD AKTEAIKDDE GKAGPSEPVS LNGVTYDFSQ NPTLEYDHRM SPV FDRRIP EEYRRDAVDI LEKIYDDEVK NRIFLKWDQE KRKQLMGDKA PNK

UniProtKB: UNIPROTKB: A0A0E2CXR9

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Macromolecule #9: DUF4468 domain-containing protein

MacromoleculeName: DUF4468 domain-containing protein / type: protein_or_peptide / ID: 9 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans (bacteria) / Strain: flaB1- KO mutant
Molecular weightTheoretical: 27.492506 KDa
SequenceString: MEKSTMKEKL FYFLILISTF AGISSQEFEP DGKVKILPYE QGQIKDLEVL GKDIVEFHKR IESRLGFLNQ RKQIQDNLYS QFIPAYEDQ IPQSRNRYML DLRFVLKVSG AGATNSPLKL ESVVFWSRKS LISKMRPQYE EISILKNDKI TNEGPNSIEL V VRKKTDSG ...String:
MEKSTMKEKL FYFLILISTF AGISSQEFEP DGKVKILPYE QGQIKDLEVL GKDIVEFHKR IESRLGFLNQ RKQIQDNLYS QFIPAYEDQ IPQSRNRYML DLRFVLKVSG AGATNSPLKL ESVVFWSRKS LISKMRPQYE EISILKNDKI TNEGPNSIEL V VRKKTDSG TKETVYNVAT IREPAQRVKL VRIYRTNLLE IIRRIDKYVE GSIKNAAEDV ETTLREVENG GPYQENPKE

UniProtKB: UNIPROTKB: Q72NA0

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Macromolecule #10: LIC_13212 protein

MacromoleculeName: LIC_13212 protein / type: protein_or_peptide / ID: 10 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans (bacteria) / Strain: flaB1- KO mutant
Molecular weightTheoretical: 32.292234 KDa
SequenceString: MRDQNFDNLN KGKSMNIRIF SFLIILTIFG LGAAPNKVLT LEEKEELRQI ETVRKGGFTD IEVDNLHASI AGNILKINNL LGNETYKKA LRYIEDEPRE AAKFLFQDKE NKQYLQLDLG LGQSFADYPK TYLYQSKIYI YPGTDGKSLE KIILQFKRTN A KGEVFIRE ...String:
MRDQNFDNLN KGKSMNIRIF SFLIILTIFG LGAAPNKVLT LEEKEELRQI ETVRKGGFTD IEVDNLHASI AGNILKINNL LGNETYKKA LRYIEDEPRE AAKFLFQDKE NKQYLQLDLG LGQSFADYPK TYLYQSKIYI YPGTDGKSLE KIILQFKRTN A KGEVFIRE MRRLINNSPK GPTFLGDGKR TPNNNSEILL EFFSSHDTDF LWPDNPIQPV PASVTTKLNE AVNPLPYNKQ KQ IILQYKR YLRKVDKMVS LRLHTMELDQ KMMISKMLEF Q

UniProtKB: UNIPROTKB: Q72MH5

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Macromolecule #11: Lipoprotein

MacromoleculeName: Lipoprotein / type: protein_or_peptide / ID: 11 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans (bacteria) / Strain: flaB1- KO mutant
Molecular weightTheoretical: 17.12867 KDa
SequenceString:
MKKILAICLL FFFALFSLQA GKSQGVVEEF NKVEEYNKNV KLSDAAKKAT LEKNLLSAVK YTLHHRYLEY KEITKDLNTD TMLYEPQKG TYTVYVKFKK YLFFYSFKMD PEIYLQTPEN EVFYLRPENL DDPHKENTSA PDGKSGK

UniProtKB: UNIPROTKB: Q72RW3

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Macromolecule #12: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 12 / Number of copies: 18 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #13: water

MacromoleculeName: water / type: ligand / ID: 13 / Number of copies: 36 / 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: 61.5 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: 4.3 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 4.2 angstroems and better resolved features in the cryoEM map
Number images used: 53501
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
Detailsiterative refinement was done in reciprocal and real space, using servalcat and phenix.real_space_refine respectively
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT / Target criteria: cross-correlation coefficient
Output model

PDB-10ll:
Native flagellar filament from Leptospira interrogans flaB1- KO mutant strain

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