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- PDB-10lm: Native flagellar filament from Leptospira biflexa -

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Basic information

Entry
Database: PDB / ID: 10lm
TitleNative flagellar filament from Leptospira biflexa
Components
  • (Flagellar Coiling Protein ...) x 2
  • FlaA2 associated protein B0STF2
  • FlaA2-associated protein FlaAP
  • Flagellar filament outer layer protein (Sheath protein) putative signal peptide
  • Flagellin
  • LEPBI_I0662 protein
  • LEPBI_I1029 protein
  • LEPBI_I3081 protein
  • LEPBI_II0033 protein
KeywordsPROTEIN FIBRIL / Bacterial Endo-flagellum / Filament
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 '
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBrady, M.R. / San Martin, F. / Sindelar, C.V. / Buschiazzo, A.
Funding supportUruguay, 1items
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, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A3: Flagellin
A4: Flagellin
A5: Flagellin
A6: Flagellin
A7: Flagellin
A8: Flagellin
B3: Flagellin
B4: Flagellin
B5: Flagellin
B6: Flagellin
B7: Flagellin
B8: Flagellin
C2: Flagellin
C3: Flagellin
C4: Flagellin
C5: Flagellin
C6: Flagellin
C7: Flagellin
C8: Flagellin
D2: Flagellin
D3: Flagellin
D4: Flagellin
D5: Flagellin
D6: Flagellin
D7: Flagellin
E1: Flagellin
E2: Flagellin
E3: Flagellin
E4: Flagellin
E5: Flagellin
E6: Flagellin
E7: Flagellin
F1: Flagellin
F2: Flagellin
F3: Flagellin
F4: Flagellin
F5: Flagellin
F6: Flagellin
G1: Flagellin
G2: Flagellin
G5: Flagellin
G6: Flagellin
G7: Flagellin
G8: Flagellin
G9: Flagellin
H5: Flagellin
H6: Flagellin
H7: Flagellin
H8: Flagellin
H9: Flagellin
I4: Flagellin
I5: Flagellin
I6: Flagellin
I7: Flagellin
I8: Flagellin
I9: Flagellin
J4: Flagellin
J5: Flagellin
J6: Flagellin
J7: Flagellin
J8: Flagellin
J9: Flagellin
K3: Flagellin
K4: Flagellin
K5: Flagellin
K6: Flagellin
K7: Flagellin
K8: Flagellin
L1: Flagellar Coiling Protein FcpA
L2: Flagellar Coiling Protein FcpA
L3: Flagellar Coiling Protein FcpA
L4: Flagellar Coiling Protein FcpA
L5: Flagellar Coiling Protein FcpA
M1: Flagellar Coiling Protein FcpA
M2: Flagellar Coiling Protein FcpA
M3: Flagellar Coiling Protein FcpA
M4: Flagellar Coiling Protein FcpA
M5: Flagellar Coiling Protein FcpA
N1: Flagellar Coiling Protein FcpA
N2: Flagellar Coiling Protein FcpA
N3: Flagellar Coiling Protein FcpA
N4: Flagellar Coiling Protein FcpA
N5: Flagellar Coiling Protein FcpA
N6: Flagellar Coiling Protein FcpA
O1: Flagellar Coiling Protein FcpA
O2: Flagellar Coiling Protein FcpA
O3: Flagellar Coiling Protein FcpA
O4: Flagellar Coiling Protein FcpA
O5: Flagellar Coiling Protein FcpA
P1: Flagellar Coiling Protein FcpA
P2: Flagellar Coiling Protein FcpA
P3: Flagellar Coiling Protein FcpA
P4: Flagellar Coiling Protein FcpA
P5: Flagellar Coiling Protein FcpA
P6: Flagellar Coiling Protein FcpA
Q1: Flagellar Coiling Protein FcpB
Q2: Flagellar Coiling Protein FcpB
Q3: Flagellar Coiling Protein FcpB
Q4: Flagellar Coiling Protein FcpB
R1: Flagellar Coiling Protein FcpB
R2: Flagellar Coiling Protein FcpB
R3: Flagellar Coiling Protein FcpB
R4: Flagellar Coiling Protein FcpB
R5: Flagellar Coiling Protein FcpB
S2: Flagellar Coiling Protein FcpB
S3: Flagellar Coiling Protein FcpB
S4: Flagellar Coiling Protein FcpB
S5: Flagellar Coiling Protein FcpB
S6: Flagellar Coiling Protein FcpB
U3: LEPBI_I1029 protein
U4: LEPBI_I1029 protein
U5: LEPBI_I1029 protein
U6: LEPBI_I1029 protein
V0: Flagellar filament outer layer protein (Sheath protein) putative signal peptide
V1: Flagellar filament outer layer protein (Sheath protein) putative signal peptide
V2: Flagellar filament outer layer protein (Sheath protein) putative signal peptide
V3: Flagellar filament outer layer protein (Sheath protein) putative signal peptide
V4: Flagellar filament outer layer protein (Sheath protein) putative signal peptide
X0: Flagellar filament outer layer protein (Sheath protein) putative signal peptide
X1: Flagellar filament outer layer protein (Sheath protein) putative signal peptide
X2: Flagellar filament outer layer protein (Sheath protein) putative signal peptide
X3: Flagellar filament outer layer protein (Sheath protein) putative signal peptide
X4: Flagellar filament outer layer protein (Sheath protein) putative signal peptide
Y1: FlaA2 associated protein B0STF2
Y2: FlaA2 associated protein B0STF2
Y3: FlaA2 associated protein B0STF2
Y4: FlaA2 associated protein B0STF2
Z0: FlaA2-associated protein FlaAP
Z1: FlaA2-associated protein FlaAP
Z2: FlaA2-associated protein FlaAP
Za: FlaA2-associated protein FlaAP
a1: LEPBI_I3081 protein
a2: LEPBI_I3081 protein
a3: LEPBI_I3081 protein
a4: LEPBI_I3081 protein
a5: LEPBI_I3081 protein
b2: LEPBI_I0662 protein
b3: LEPBI_I0662 protein
b4: LEPBI_I0662 protein
c1: LEPBI_II0033 protein
c2: LEPBI_II0033 protein
c3: LEPBI_II0033 protein
h0: Flagellin
i0: Flagellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,631,397154
Polymers4,630,996144
Non-polymers40110
Water36020
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 8 types, 103 molecules A3A4A5A6A7A8B3B4B5B6B7B8C2C3C4C5C6C7C8D2D3D4D5D6D7E1E2E3E4E5...

#1: Protein ...
Flagellin


Mass: 31415.635 Da / Num. of mol.: 70 / Source method: isolated from a natural source
Source: (natural) Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
References: UniProt: B0SQZ5
#4: Protein
LEPBI_I1029 protein


Mass: 37285.012 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
References: UniProt: B0SMK8
#5: Protein
Flagellar filament outer layer protein (Sheath protein) putative signal peptide


Mass: 27630.594 Da / Num. of mol.: 10 / Source method: isolated from a natural source
Source: (natural) Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
References: UniProt: B0SKT5
#6: Protein
FlaA2 associated protein B0STF2


Mass: 33018.371 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
References: UniProt: B0STF2
#7: Protein
FlaA2-associated protein FlaAP


Mass: 43060.012 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
References: UniProt: B0SJC6
#8: Protein
LEPBI_I3081 protein


Mass: 27089.711 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
References: UniProt: B0SPP1
#9: Protein LEPBI_I0662 protein


Mass: 31206.863 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
References: UniProt: B0SKN8
#10: Protein LEPBI_II0033 protein


Mass: 20826.744 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
References: UniProt: B0STN7

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Flagellar Coiling Protein ... , 2 types, 41 molecules L1L2L3L4L5M1M2M3M4M5N1N2N3N4N5N6O1O2O3O4O5P1P2P3P4P5P6Q1Q2Q3...

#2: Protein ...
Flagellar Coiling Protein FcpA


Mass: 35876.797 Da / Num. of mol.: 27 / Source method: isolated from a natural source
Source: (natural) Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
References: UniProt: B0STJ8
#3: Protein
Flagellar Coiling Protein FcpB


Mass: 31565.652 Da / Num. of mol.: 14 / Source method: isolated from a natural source
Source: (natural) Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
References: UniProt: B0SR03

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Non-polymers , 2 types, 30 molecules

#11: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: native flagellar filament / Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 25.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARCparticle selectionFilament Tracer
7Coot1.1.19model fitting
8UCSF ChimeraX1.10.1model fitting
10PHENIX2.0-5936model refinementreal_space_refine
11Servalcat0.4.128model refinement
12cryoSPARCinitial Euler assignment
13cryoSPARCfinal Euler assignment
15cryoSPARC4.2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176558
Details: Further Density Modification with Phenix Resolve increased resolution to 3.2 angstroems and better resolved features in the cryoEM map
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL
Details: iteration between real space refinement with Phenix.real_space_refine, and Servalcat (reciprocal space)
Atomic model buildingDetails: we used comparative proteomics (wt and mutants) plus cross-linked+MS data; AlphaFold-redicted Initial models; and crystallographic structures
Source name: Other / Type: integrative model

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