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- EMDB-62928: Cryo-EM structure of Shewanella oneidensis MR-1 flagella. -

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Basic information

Entry
Database: EMDB / ID: EMD-62928
TitleCryo-EM structure of Shewanella oneidensis MR-1 flagella.
Map data
Sample
  • Cell: Shewanella oneidensis MR-1 Flagella
    • Protein or peptide: Flagellin
Keywordsthe filaments of bacterial flagella.bacteria movement / PROTEIN FIBRIL
Function / homology
Function and homology information


bacterial-type flagellum / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region
Similarity search - Function
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
Biological speciesShewanella oneidensis MR-1 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsLi DN / Liu C / Li D / Dai B
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of Shewanella oneidensis MR-1 flagella.
Authors: Li DN / Liu C
History
DepositionJan 2, 2025-
Header (metadata) releaseJan 7, 2026-
Map releaseJan 7, 2026-
UpdateJan 7, 2026-
Current statusJan 7, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62928.png

Downloads & links

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Map

FileDownload / File: emd_62928.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.007749507 - 0.02275875
Average (Standard dev.)0.0006164909 (±0.002199669)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62928_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_62928_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 : Shewanella oneidensis MR-1 Flagella

EntireName: Shewanella oneidensis MR-1 Flagella
Components
  • Cell: Shewanella oneidensis MR-1 Flagella
    • Protein or peptide: Flagellin

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Supramolecule #1: Shewanella oneidensis MR-1 Flagella

SupramoleculeName: Shewanella oneidensis MR-1 Flagella / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)
Molecular weightTheoretical: 28.495861 KDa
SequenceString: MAITVNTNVT SLKAQKNLNT SASDLATSME RLSSGLRINS AKDDAAGLAI SNRLNSQVRG LEVGMRNAND AISIAQIAEG AMQEQTNML QRMRDLTVQS ENGANSSADL SALKAEMDQL ANEIDEIGKT TAFGTTKLLA GGFSAGKNFQ VGAQDGEDIK V TVKASNKS ...String:
MAITVNTNVT SLKAQKNLNT SASDLATSME RLSSGLRINS AKDDAAGLAI SNRLNSQVRG LEVGMRNAND AISIAQIAEG AMQEQTNML QRMRDLTVQS ENGANSSADL SALKAEMDQL ANEIDEIGKT TAFGTTKLLA GGFSAGKNFQ VGAQDGEDIK V TVKASNKS SLSVGSLGNT TSAARASSLK KIDAAIKTID AQRADLGAIQ NRLAHNISNS ANTQANVADA KSRIVDVDFA KE TSQMTKN QVLQQTGSAM LAQANQLPQV ALSLL

UniProtKB: Flagellin

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI 12
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 65.4 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53990
CTF correctionType: NONE
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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