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- EMDB-63347: Straight and symmetrical filament of the spirochete periplasmic f... -

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Basic information

Entry
Database: EMDB / ID: EMD-63347
TitleStraight and symmetrical filament of the spirochete periplasmic flagella of Leptospira biflexa
Map data
Sample
  • Complex: Straight and symmetrical filament of the spirochete periplasmic flagella
    • Protein or peptide: Flagellin
    • Protein or peptide: Bacterial flagellar sheath protein
    • Protein or peptide: Bacterial flagellar sheath protein
KeywordsFilament / Flagellar motor / MOTOR PROTEIN
Function / homology: / : / Uncharacterized protein
Function and homology information
Biological speciesLeptospira biflexa (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.3 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_63347.png

Downloads & links

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Map

FileDownload / File: emd_63347.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: 0.0434
Minimum - Maximum-0.25791273 - 0.45176083
Average (Standard dev.)0.000054460073 (±0.004953712)
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_63347_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63347_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63347_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 : Straight and symmetrical filament of the spirochete periplasmic f...

EntireName: Straight and symmetrical filament of the spirochete periplasmic flagella
Components
  • Complex: Straight and symmetrical filament of the spirochete periplasmic flagella
    • Protein or peptide: Flagellin
    • Protein or peptide: Bacterial flagellar sheath protein
    • Protein or peptide: Bacterial flagellar sheath protein

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Supramolecule #1: Straight and symmetrical filament of the spirochete periplasmic f...

SupramoleculeName: Straight and symmetrical 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: 31.415635 KDa
SequenceString: MIINHNVSAI FAHRTLKSND ANLSKDIEKL SSGMRINKAG DDASGLAVSE KMRTQIAGLR RAEQNTEDGM SLIQTAEGYL QETHEIVQR VRVLAVQAAN GIYSEEDRQQ IQVEVSQLVD EIDRIASQAE FNKMKLLTGA FARLNPTASM WFHIGANMHQ R ERVYIETM ...String:
MIINHNVSAI FAHRTLKSND ANLSKDIEKL SSGMRINKAG DDASGLAVSE KMRTQIAGLR RAEQNTEDGM SLIQTAEGYL QETHEIVQR VRVLAVQAAN GIYSEEDRQQ IQVEVSQLVD EIDRIASQAE FNKMKLLTGA FARLNPTASM WFHIGANMHQ R ERVYIETM NTAALGLRNP TVLTFISLST AGKANSVIGL CDDALRVISK QRADLGAYYN RMEHAAKGLM NAYENTQASE SR IRDTDMA EQMTSFTRYQ ILTQAATSML AQANMKSQSV MRLLQ

UniProtKB: UNIPROTKB: A0AAQ2CUK9

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Macromolecule #2: Bacterial flagellar sheath protein

MacromoleculeName: Bacterial flagellar sheath protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Leptospira biflexa (bacteria)
Molecular weightTheoretical: 31.565652 KDa
SequenceString: MKIKLILPIL LLSIGVFAQT GSSETGSTSA GIDPSQSGKS MADTEKELDD NISEVNKRLR LHTVLFKMKV RTLPHKTVLY KGKPSADGE RCEAADKQEA QDNTCLHLEV FDFVGSEDGK SSKNLGAKFK KMELFFEGSN NADPDPRKEQ PRNLTKIRTY I YQNNFLLE ...String:
MKIKLILPIL LLSIGVFAQT GSSETGSTSA GIDPSQSGKS MADTEKELDD NISEVNKRLR LHTVLFKMKV RTLPHKTVLY KGKPSADGE RCEAADKQEA QDNTCLHLEV FDFVGSEDGK SSKNLGAKFK KMELFFEGSN NADPDPRKEQ PRNLTKIRTY I YQNNFLLE DKVISVIADV APNGEPAHND KIELFYQHDD YPVWGTPETP SEKGVGKYIL SNVENTKSNP IRNNFKKQFY FK NLDYFDK LFTKIFDYND RDSNKHYKKN VEALKGSLKY

UniProtKB: Uncharacterized protein

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Macromolecule #3: Bacterial flagellar sheath protein

MacromoleculeName: Bacterial flagellar sheath protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Leptospira biflexa (bacteria)
Molecular weightTheoretical: 35.876797 KDa
SequenceString: MKIIKYLLIL QLVSGFSVLF AQTQPANAQE SQAAKDQVDE LLKGELVPEN DDAELTEDQK KKKKEIMEQE SLWKNPDFKG YNKTFQELH QLSKTFANNQ FRLALSNYQS GVNTIMKNRD WVEQYRKEEA EKKRLDEKWY WQKVDRKARE ERVVYREKMK A KQDALNYF ...String:
MKIIKYLLIL QLVSGFSVLF AQTQPANAQE SQAAKDQVDE LLKGELVPEN DDAELTEDQK KKKKEIMEQE SLWKNPDFKG YNKTFQELH QLSKTFANNQ FRLALSNYQS GVNTIMKNRD WVEQYRKEEA EKKRLDEKWY WQKVDRKARE ERVVYREKMK A KQDALNYF SKAINHLDEI KNPDLRERPE FKRLLSDVYR SWIMAEYDLQ NLPQTIPILE LYIEIDDNEK EYPAHKYLAS AY SFEENMI KKTKGPDDML FKYRYKKNVH LLRATELKYG KDSPEYKHIV NVINRDEVIS VAQ

UniProtKB: UNIPROTKB: A0AAQ2CSE7

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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
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: 4.836 Å
Applied symmetry - Helical parameters - Δ&Phi: 65.425 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 138670
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: 45.5861
Output model

PDB-9lry:
Straight and symmetrical filament of the spirochete periplasmic flagella of Leptospira biflexa

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