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- EMDB-75268: Native flagellar filament from Leptospira interrogans -

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Basic information

Entry
Database: EMDB / ID: EMD-75268
TitleNative flagellar filament from Leptospira interrogans
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


: / : / : / : / : / Uncharacterized protein / : / : / : / :
Similarity search - Component
Biological speciesLeptospira interrogans serovar Copenhageni (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 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_75268.png

Downloads & links

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Map

FileDownload / File: emd_75268.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-0.23983586 - 0.4574863
Average (Standard dev.)-0.00000000000027 (±0.03954105)
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_75268_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_75268_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 A (FcpA)
    • Protein or peptide: Flagellar Coiling Protein B (FcpB)
    • Protein or peptide: Flagellar filament sheath protein
    • Protein or peptide: Flagellar filament sheath protein
    • Protein or peptide: FlaA2 associated protein 2
    • Protein or peptide: FlaA2-associated protein 1 (FlaAP)
    • Protein or peptide: DUF4468 domain-containing protein
    • Protein or peptide: Lipoprotein
    • Protein or peptide: HEAT repeat domain-containing 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 interrogans serovar Copenhageni (bacteria)
Strain: Fiocruz L1-130

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Details: part of the native flagellar filament assembly / Number of copies: 64 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans serovar Copenhageni (bacteria)
Strain: Fiocruz L1-130
Molecular weightTheoretical: 31.341467 KDa
SequenceString: MIINHNLAAI NSHRVLKFQN NEVAKNMETL SSGMRINRAG DDASGLAVSE KMRTQVKGLR QAERNTEDGM SLIQTTEGYL QETNDIIQR IRVLAIQSSN GIYSAEDRQM IQVEVSQLVD EIDRIASQAE FNKMALLQGD FARGSRTSSM WFHIGPNQHQ R ERVYIATM ...String:
MIINHNLAAI NSHRVLKFQN NEVAKNMETL SSGMRINRAG DDASGLAVSE KMRTQVKGLR QAERNTEDGM SLIQTTEGYL QETNDIIQR IRVLAIQSSN GIYSAEDRQM IQVEVSQLVD EIDRIASQAE FNKMALLQGD FARGSRTSSM WFHIGPNQHQ R ERVYIATM TAKSLNLIKA DGSLLTLSTA EFANDAIGTL DDALMKINKQ RANLGAYFNR LEHASKGLMV AYENIQASES RI RDTDMAE ETVAFTKNQI LVQSGTAMLA QANVRPQSVL QLLR

UniProtKB: UNIPROTKB: Q72R58

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Macromolecule #2: Flagellar Coiling Protein A (FcpA)

MacromoleculeName: Flagellar Coiling Protein A (FcpA) / type: protein_or_peptide / ID: 2 / Details: Part or the native flagellar filament assembly / Number of copies: 29 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans serovar Copenhageni (bacteria)
Strain: Fiocruz L1-130
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 B (FcpB)

MacromoleculeName: Flagellar Coiling Protein B (FcpB) / type: protein_or_peptide / ID: 3 / Details: Part of the native flagellar filament assembly / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans serovar Copenhageni (bacteria)
Strain: Fiocruz L1-130
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 / Details: Part of the native flagellar filament assembly / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans serovar Copenhageni (bacteria)
Strain: Fiocruz L1-130
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: Flagellar filament sheath protein

MacromoleculeName: Flagellar filament sheath protein / type: protein_or_peptide / ID: 5 / Details: Part of the native flagellar filament assembly / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans serovar Copenhageni (bacteria)
Strain: Fiocruz L1-130
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: Q72U75

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Macromolecule #6: FlaA2 associated protein 2

MacromoleculeName: FlaA2 associated protein 2 / type: protein_or_peptide / ID: 6 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans serovar Copenhageni (bacteria)
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: A0AAV9FRP0

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Macromolecule #7: FlaA2-associated protein 1 (FlaAP)

MacromoleculeName: FlaA2-associated protein 1 (FlaAP) / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans serovar Copenhageni (bacteria)
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: Q72SU9

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Macromolecule #8: DUF4468 domain-containing protein

MacromoleculeName: DUF4468 domain-containing protein / type: protein_or_peptide / ID: 8 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans serovar Copenhageni (bacteria)
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 #9: Lipoprotein

MacromoleculeName: Lipoprotein / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans serovar Copenhageni (bacteria)
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 #10: HEAT repeat domain-containing protein

MacromoleculeName: HEAT repeat domain-containing protein / type: protein_or_peptide / ID: 10 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Leptospira interrogans serovar Copenhageni (bacteria)
Molecular weightTheoretical: 33.181207 KDa
SequenceString: MFKNISISII LFSISILPLF SSDKAIEYAD RAYFEQIRKL ESGSYEEKVD AADYLKFVNN KLAVRPLINA LRGNPKIPKS LENHPYLKF TVAQALAVID HVDAIKPTIE EYKKLEPTIQ EKDEPYFTSR EDYTMVIAAG EILRTIGSYP YMKESEEVLV N ALGHTNYY ...String:
MFKNISISII LFSISILPLF SSDKAIEYAD RAYFEQIRKL ESGSYEEKVD AADYLKFVNN KLAVRPLINA LRGNPKIPKS LENHPYLKF TVAQALAVID HVDAIKPTIE EYKKLEPTIQ EKDEPYFTSR EDYTMVIAAG EILRTIGSYP YMKESEEVLV N ALGHTNYY IRASAADGLK YMNRKETVNF LVSTLEKEKN EFTKAAILNA IVNIMKVADK SFYSLCDMLK SENPSVRYRT SM ALGEVDL KAAEFYLRQA LLVEDKQNVR DQIRKDLASV LGFKLPTISV IFAE

UniProtKB: UNIPROTKB: Q72MR9

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Macromolecule #11: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 11 / Number of copies: 18 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #12: water

MacromoleculeName: water / type: ligand / ID: 12 / 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: 3.0 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
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 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: 35760
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: projection matching
Final angle assignmentType: MAXIMUM LIKELIHOOD
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
SoftwareName: Coot (ver. 1.1.19)
DetailsRefinement iterated between real space (phenix.real_space_refine) and reciprocal space (Servalcat)
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-10lk:
Native flagellar filament from Leptospira interrogans

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