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- EMDB-49126: In situ unsheathed flagellar filament of Vibrio cholerae resolved... -

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Basic information

Entry
Database: EMDB / ID: EMD-49126
TitleIn situ unsheathed flagellar filament of Vibrio cholerae resolved with helical reconstruction.
Map dataIn situ unsheathed flagellar filament with helical reconstruction
Sample
  • Cell: Vibrio cholerae serotype O1
    • Protein or peptide: Flagellin D
KeywordsIn situ cryo-EM / unsheathed flagellar filament / FlaD Vibrio cholerae. / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
Flagellin hook, IN motif / Flagellin hook IN motif / 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 speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsWangbiao G / Jun L
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI087946 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI132818 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of the sheathed flagellum in intact Vibrio cholerae
Authors: Wangbiao G / Sarah Z / Jian Y / Jin HP / Venus S / Shenping W / Karl EK / Fitnat Y / Jun L
History
DepositionFeb 8, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49126.png

Downloads & links

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Map

FileDownload / File: emd_49126.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn situ unsheathed flagellar filament with helical reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 448 pix.
= 478.464 Å		1.07 Å/pix.
x 448 pix.
= 478.464 Å		1.07 Å/pix.
x 448 pix.
= 478.464 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.26665437 - 0.5796193
Average (Standard dev.)0.0012750364 (±0.033426993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 478.464 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49126_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: In situ unsheathed flagellar filament with helical reconstruction

Fileemd_49126_half_map_1.map
AnnotationIn situ unsheathed flagellar filament with helical reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: In situ unsheathed flagellar filament with helical reconstruction

Fileemd_49126_half_map_2.map
AnnotationIn situ unsheathed flagellar filament with helical reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Vibrio cholerae serotype O1

EntireName: Vibrio cholerae serotype O1 (bacteria)
Components
  • Cell: Vibrio cholerae serotype O1
    • Protein or peptide: Flagellin D

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Supramolecule #1: Vibrio cholerae serotype O1

SupramoleculeName: Vibrio cholerae serotype O1 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)

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Macromolecule #1: Flagellin D

MacromoleculeName: Flagellin D / type: protein_or_peptide / ID: 1 / Number of copies: 33 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 39.808809 KDa
Recombinant expressionOrganism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
SequenceString: AVNVNTNVAA MTAQRYLTGA TNAQQTSMER LSSGFKINSA KDDAAGLQIS NRLNVQSRGL DVAVRNANDG ISIAQTAEGA MNETTNILQ RMRDLSLQSA NGSNSKSERV AIQEEITALN DELNRIAETT SFGGNKLLNG TFSTKSFQIG ADNGEAVMLT L KDMRSDNR ...String:
AVNVNTNVAA MTAQRYLTGA TNAQQTSMER LSSGFKINSA KDDAAGLQIS NRLNVQSRGL DVAVRNANDG ISIAQTAEGA MNETTNILQ RMRDLSLQSA NGSNSKSERV AIQEEITALN DELNRIAETT SFGGNKLLNG TFSTKSFQIG ADNGEAVMLT L KDMRSDNR MMGGTSYVAA EGKDKDWKVQ AGANDITFTL KDIDGNDQTI TVNAKEGDDI EEVATYINGQ TDMVKASVNE KG QLQIFAG NNKVTGDVAF SGGLAGALNM QAGTAETVDT IDVTSVGGAQ QSVAVIDSAL KYVDSHRAEL GAFQNRFNHA ISN LDNINE NVNASKSRIK DTDFAKETTA LTKSQILSQA SSSVLAQAKQ APNAALSLLG

UniProtKB: Flagellin D

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statecell

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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: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.74 Å
Applied symmetry - Helical parameters - Δ&Phi: 65.41 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103479
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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