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- EMDB-76766: H-ring in Vibrio cholerae at closed state of P-ring -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-76766
TitleH-ring in Vibrio cholerae at closed state of P-ring
Map data
Sample
  • Cell: Vibrio cholerae DflhG
KeywordsVibrio cholerae / FigT / FlgP / Open state / MOTOR PROTEIN
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsGuo WB / Yue J / Liu J
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI189907 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37AI102584 United States
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: Sheathed flagellar motor structure with C1 symmetry in Vibrio cholerae
Authors: Guo WB / Yue J / Liu J
History
DepositionApr 19, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76766.png

Downloads & links

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Map

FileDownload / File: emd_76766.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 512 pix.
= 769.024 Å		1.5 Å/pix.
x 512 pix.
= 769.024 Å		1.5 Å/pix.
x 512 pix.
= 769.024 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.502 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.9390419 - 1.4156082
Average (Standard dev.)0.0033713423 (±0.044920083)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 769.024 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_76766_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_76766_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_76766_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Vibrio cholerae DflhG

EntireName: Vibrio cholerae DflhG
Components
  • Cell: Vibrio cholerae DflhG

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Supramolecule #1: Vibrio cholerae DflhG

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

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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

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 opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C58 (58 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 24036
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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