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- EMDB-49125: In situ structure of the sheathed FlaD flagellar filament in Vibr... -

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Basic information

Entry
Database: EMDB / ID: EMD-49125
TitleIn situ structure of the sheathed FlaD flagellar filament in Vibrio cholerae
Map dataIn situ structure of the sheathed FlaD flagellar filament in Vibrio cholerae.
Sample
  • Cell: Vibrio cholerae
    • Protein or peptide: Flagellin D
KeywordsIn situ cryo-EM / sheathed 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 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_49125.png

Downloads & links

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Map

FileDownload / File: emd_49125.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn situ structure of the sheathed FlaD flagellar filament in Vibrio cholerae.
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: 0.12
Minimum - Maximum-0.69462335 - 1.1522717
Average (Standard dev.)0.0069333734 (±0.04201892)
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_49125_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: In situ structure of the sheathed FlaD flagellar...

Fileemd_49125_half_map_1.map
AnnotationIn situ structure of the sheathed FlaD flagellar filament in Vibrio cholerae.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: In situ structure of the sheathed FlaD flagellar...

Fileemd_49125_half_map_2.map
AnnotationIn situ structure of the sheathed FlaD flagellar filament in Vibrio cholerae.
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

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

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Supramolecule #1: Vibrio cholerae

SupramoleculeName: Vibrio cholerae / 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: 39.940008 KDa
Recombinant expressionOrganism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
SequenceString: MAVNVNTNVA AMTAQRYLTG ATNAQQTSME RLSSGFKINS AKDDAAGLQI SNRLNVQSRG LDVAVRNAND GISIAQTAEG AMNETTNIL QRMRDLSLQS ANGSNSKSER VAIQEEITAL NDELNRIAET TSFGGNKLLN GTFSTKSFQI GADNGEAVML T LKDMRSDN ...String:
MAVNVNTNVA AMTAQRYLTG ATNAQQTSME RLSSGFKINS AKDDAAGLQI SNRLNVQSRG LDVAVRNAND GISIAQTAEG AMNETTNIL QRMRDLSLQS ANGSNSKSER VAIQEEITAL NDELNRIAET TSFGGNKLLN GTFSTKSFQI GADNGEAVML T LKDMRSDN RMMGGTSYVA AEGKDKDWKV QAGANDITFT LKDIDGNDQT ITVNAKEGDD IEEVATYING QTDMVKASVN EK GQLQIFA GNNKVTGDVA FSGGLAGALN MQAGTAETVD TIDVTSVGGA QQSVAVIDSA LKYVDSHRAE LGAFQNRFNH AIS NLDNIN ENVNASKSRI KDTDFAKETT ALTKSQILSQ ASSSVLAQAK QAPNAALSLL G

UniProtKB: Flagellin D

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TECNAI F30
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: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2331318
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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