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- EMDB-66642: core filament of the spirochete periplasmic flagella of Leptospir... -

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Basic information

Entry
Database: EMDB / ID: EMD-66642
Titlecore filament of the spirochete periplasmic flagella of Leptospira biflexa from the flaA2-complemented stain
Map data
Sample
  • Complex: core filament of the spirochete periplasmic flagella from the flaA2-complemented strain
    • Protein or peptide: Flagellin
KeywordsFilament / Flagellar motor / MOTOR PROTEIN
Function / homologyperiplasmic flagellum / 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 / structural molecule activity / Flagellin
Function and homology information
Biological speciesLeptospira biflexa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 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: To Be Published
Title: Cooperativity of sheath proteins in the flagellar assembly of Leptospira spirochete
Authors: Kawamoto A / Kuribayashi T / Morita M / Nakamura S / Koizumi N
History
DepositionOct 17, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66642.png

Downloads & links

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Map

FileDownload / File: emd_66642.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 384 pix.
= 445.44 Å		1.16 Å/pix.
x 384 pix.
= 445.44 Å		1.16 Å/pix.
x 384 pix.
= 445.44 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.512
Minimum - Maximum-0.8188733 - 1.6973878
Average (Standard dev.)0.0028539354 (±0.046637174)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 445.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66642_msk_1.map
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Additional map: #1

Fileemd_66642_additional_1.map
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Half map: #1

Fileemd_66642_half_map_1.map
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Half map: #2

Fileemd_66642_half_map_2.map
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Sample components

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Entire : core filament of the spirochete periplasmic flagella from the fla...

EntireName: core filament of the spirochete periplasmic flagella from the flaA2-complemented strain
Components
  • Complex: core filament of the spirochete periplasmic flagella from the flaA2-complemented strain
    • Protein or peptide: Flagellin

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Supramolecule #1: core filament of the spirochete periplasmic flagella from the fla...

SupramoleculeName: core filament of the spirochete periplasmic flagella from the flaA2-complemented strain
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: 31.269217 KDa
SequenceString: MIINHNLAAI NSHRVLKFQN EEVSKNMEKL SSGMRINRAG DDASGLAVSE KMRTQVNGLR QAERNTEDGM SLIQTTEGFL QESNDIIQR IRTLAIQSSN GIYTEEDRQM IQVEVSQLID EVDRIASQAE FNKMNLLQGD FARGSRATSM WFHIGPNMHQ R ERVFIATM ...String:
MIINHNLAAI NSHRVLKFQN EEVSKNMEKL SSGMRINRAG DDASGLAVSE KMRTQVNGLR QAERNTEDGM SLIQTTEGFL QESNDIIQR IRTLAIQSSN GIYTEEDRQM IQVEVSQLID EVDRIASQAE FNKMNLLQGD FARGSRATSM WFHIGPNMHQ R ERVFIATM TARSLNLKGQ SGELLSLSTA DKSNDAIGTL DAALTRISKQ RANLGAYFNR LEHAAKGLMN AYENTQASES RI RDADMAE ETVAFTKNQI LVQSGTAMLA QANVRPQGVL SLLR

UniProtKB: Flagellin

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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
Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 14160 / Average exposure time: 3.782 sec. / Average electron dose: 40.0 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: 81000
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: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 457214
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: NOT APPLICABLE / 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-9x7l:
core filament of the spirochete periplasmic flagella of Leptospira biflexa from the flaA2-complemented stain

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