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- EMDB-52337: Cryo-EM structure of the wild-type flagellar filament from Rosebu... -

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Basic information

Entry
Database: EMDB / ID: EMD-52337
TitleCryo-EM structure of the wild-type flagellar filament from Roseburia hominis
Map dataUnfiltered post-processed map from half-map 1 generated with Relion
Sample
  • Organelle or cellular component: Wild-type flagellar filament of the commensal bacteria Roseburia hominis
    • Protein or peptide: Flagellin
KeywordsFlagellin / Helical / Filament / Commensal / 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 speciesRoseburia hominis (bacteria) / Roseburia hominis A2-183 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsBell MEW / Koch I / Hipp K / Hartmann MD / Merino F / Ley RE
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of the wild-type flagellar filament from Roseburia hominis
Authors: Bell MEW / Ley RE
History
DepositionDec 16, 2024-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52337.png

Downloads & links

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Map

FileDownload / File: emd_52337.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnfiltered post-processed map from half-map 1 generated with Relion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 384 pix.
= 360.96 Å		0.94 Å/pix.
x 384 pix.
= 360.96 Å		0.94 Å/pix.
x 384 pix.
= 360.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.062041942 - 0.09514337
Average (Standard dev.)0.0000061606866 (±0.0052917525)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 360.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52337_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 3D refinement half-map 1 generated with Relion

Fileemd_52337_half_map_1.map
Annotation3D refinement half-map 1 generated with Relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 3D refinement half-map 2 generated with Relion

Fileemd_52337_half_map_2.map
Annotation3D refinement half-map 2 generated with Relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Wild-type flagellar filament of the commensal bacteria Roseburia ...

EntireName: Wild-type flagellar filament of the commensal bacteria Roseburia hominis
Components
  • Organelle or cellular component: Wild-type flagellar filament of the commensal bacteria Roseburia hominis
    • Protein or peptide: Flagellin

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Supramolecule #1: Wild-type flagellar filament of the commensal bacteria Roseburia ...

SupramoleculeName: Wild-type flagellar filament of the commensal bacteria Roseburia hominis
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Flagellar filament segment complex comprised of 22 FlaB flagellin proteins
Source (natural)Organism: Roseburia hominis (bacteria) / Strain: A2-183 / Location in cell: Bacterial flagellum

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1
Details: Complex comprised of identical flagellin monomers. The density lacked the hyper-variable domains, which were omitted from structure building.
Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Roseburia hominis A2-183 (bacteria)
Molecular weightTheoretical: 28.620791 KDa
SequenceString: MVVQHNLTAM NANRQLGITT GAQAKSSEKL SSGYKINRAA DDAAGLTISE KMRSQVRGLN KASDNAQDGV SLIQVAEGAL SETHSILQR MNELATQAAN DTNTTSDRTA VQQEINQLAS EITRIASTTQ FNTMNLIDGN FTSKKLQVGS LCGQAITIDI S DMSATGLG ...String:
MVVQHNLTAM NANRQLGITT GAQAKSSEKL SSGYKINRAA DDAAGLTISE KMRSQVRGLN KASDNAQDGV SLIQVAEGAL SETHSILQR MNELATQAAN DTNTTSDRTA VQQEINQLAS EITRIASTTQ FNTMNLIDGN FTSKKLQVGS LCGQAITIDI S DMSATGLG VSGLVVSSFS AAGKAMSAAQ DAISYVSSMR SKLGALQNRL EHTISNLDNI SENTSSAESR IRDTDMAEEM VE YSKNNIL AQAGQSMLAQ ANQSTQGVLS LLQ

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: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClSodium chloride
2.7 mMKClPotassium chloride
10.0 mMNa2HPO4Disodium phosphate
1.8 mMKH2PO4Monopotassium phosphate

Details: PBS buffer was from a stock solution (Gibco #10010031). Formula: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, and 1.8 mM KH2PO4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 281 K / Instrument: LEICA EM GP
DetailsThe specimens were sheared from wild-type culture, purified with a sucrose gradient, then washed and resuspended in PBS before imaging.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 2480 / Average electron dose: 39.0 e/Å2
Electron beamAcceleration voltage: 200 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 / Nominal magnification: 150000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 45
Applied symmetry - Helical parameters - Δz: 4.69 Å
Applied symmetry - Helical parameters - Δ&Phi: 65.4424 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 443605
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.13)
Software - details: CTFFind4 through Transphire was used to apply Motion correction & CTF correction to extracted segments.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 576587 / Software - Name: crYOLO (ver. 1.8.2)
Software - details: crYOLO was used to automatically select helical segments
Details: Particles were picked automatically using helical picking with crYOLO
Startup modelType of model: INSILICO MODEL
In silico model: Initial model was based on a hollow cylinder as a reference.
Details: An in-silico hollow cylinder was generated with EMAN/SPHIRE using the following command: sp_mask.py 'LowPassJob133_10A.mrc' 'sp_mask11' --overwrite --pixel_size=0.94 --threshold='0.00645' -- ...Details: An in-silico hollow cylinder was generated with EMAN/SPHIRE using the following command: sp_mask.py 'LowPassJob133_10A.mrc' 'sp_mask11' --overwrite --pixel_size=0.94 --threshold='0.00645' --ndilation=8 --edge_width=10 --second_mask_shape='cylinder' --s_radius='160' --s_nx='326' --s_ndilation=0 --s_edge_width=20 --fill_mask
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9hpz:
Cryo-EM structure of the wild-type flagellar filament from Roseburia hominis

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