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- EMDB-63348: Core filament of the spirochete periplasmic flagella of Leptospir... -

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Basic information

Entry
Database: EMDB / ID: EMD-63348
TitleCore filament of the spirochete periplasmic flagella of Leptospira biflexa
Map data
Sample
  • Complex: Core filament of the spirochete periplasmic flagella
    • Protein or peptide: Flagellin
KeywordsFilament / Flagellar motor / MOTOR PROTEIN
Function / homology:
Function and homology information
Biological speciesLeptospira biflexa (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.4 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
DepositionFeb 2, 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_63348.png

Downloads & links

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Map

FileDownload / File: emd_63348.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 360 pix.
= 406.8 Å		1.13 Å/pix.
x 360 pix.
= 406.8 Å		1.13 Å/pix.
x 360 pix.
= 406.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0456
Minimum - Maximum-0.21063094 - 0.3799992
Average (Standard dev.)0.000017646887 (±0.002387181)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 406.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_63348_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63348_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_63348_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 : Core filament of the spirochete periplasmic flagella

EntireName: Core filament of the spirochete periplasmic flagella
Components
  • Complex: Core filament of the spirochete periplasmic flagella
    • Protein or peptide: Flagellin

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Supramolecule #1: Core filament of the spirochete periplasmic flagella

SupramoleculeName: Core filament of the spirochete periplasmic flagella / 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: 1 / 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: UNIPROTKB: A0AAQ2CSU7

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
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
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 2318 / Average exposure time: 84.18 sec. / Average electron dose: 50.0 e/Å2
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: 59000
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

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.79 Å
Applied symmetry - Helical parameters - Δ&Phi: 65.4061 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 273749
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 46.18
Output model

PDB-9lrz:
Core filament of the spirochete periplasmic flagella of Leptospira biflexa

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