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- EMDB-70985: CryoEM structure of FlaA filament from Shewanella oneidensis -

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Basic information

Entry
Database: EMDB / ID: EMD-70985
TitleCryoEM structure of FlaA filament from Shewanella oneidensis
Map dataThe above primary density map was upsampled from a pixel size of 1.1 A to 1.0 A
Sample
  • Complex: FlaA filament
    • Protein or peptide: Flagellin
KeywordsFlaA filament / STRUCTURAL PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsQing L / Fan HC / Liu Y / Miller JF / Huang Y / Zhou ZH
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
National Institutes of Health/Office of the Director1S10OD018111 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
CitationJournal: Acs Nano / Year: 2025
Title: Curvature Generation and Engineering Principles from Shewanella oneidensis Multi-flagellin Flagellum
Authors: Lou Q / Fan H / Liu Y / Miller JF / Huang Y / Zhou ZH
History
DepositionJun 3, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70985.png

Downloads & links

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Map

FileDownload / File: emd_70985.map.gz / Format: CCP4 / Size: 479.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe above primary density map was upsampled from a pixel size of 1.1 A to 1.0 A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 501 pix.
= 501. Å		1 Å/pix.
x 501 pix.
= 501. Å		1 Å/pix.
x 501 pix.
= 501. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-0.3510957 - 20.416857
Average (Standard dev.)0.081479214 (±0.8074467)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions501501501
Spacing501501501
CellA=B=C: 501.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_70985_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_70985_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FlaA filament

EntireName: FlaA filament
Components
  • Complex: FlaA filament
    • Protein or peptide: Flagellin

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Supramolecule #1: FlaA filament

SupramoleculeName: FlaA filament / type: complex / 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: 45 / Enantiomer: LEVO
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)
Molecular weightTheoretical: 28.569881 KDa
SequenceString: AITVNTNVTS MKAQKNLNTS NSGLSTSMER LSSGLRINSA KDDAAGLAIS NRLNSQVRGL EVGMRNANDA ISIAQIAEGA MQEQTNMLQ RMRDLTIQSE NGANSTADLV SIKAEMDQLA TEIDSIGNST AFGNTKLLTG TFSAGKVFQV GHQEGEDIKV T VKASNKTS ...String:
AITVNTNVTS MKAQKNLNTS NSGLSTSMER LSSGLRINSA KDDAAGLAIS NRLNSQVRGL EVGMRNANDA ISIAQIAEGA MQEQTNMLQ RMRDLTIQSE NGANSTADLV SIKAEMDQLA TEIDSIGNST AFGNTKLLTG TFSAGKVFQV GHQEGEDIKV T VKASNKTS LSVGALNNAT SANRASSLAK IDAAIKTIDS QRADLGAVQN RLAHNISNSA NTQANVADAK SRIVDVDFAK ET SAMTKYQ VLQQTGSAML AQANQLPQVA LSLLG

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: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 4596
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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