[English] 日本語
Yorodumi
- EMDB-72840: RBM3 domain of FliF protein in MS-ring of flagellar motor in Vibr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72840
TitleRBM3 domain of FliF protein in MS-ring of flagellar motor in Vibrio cholerae
Map dataRBM3 of FliF protin in MSring of flagellar motor in Vibrio cholerae.
Sample
  • Cell: Vibrio cholerae
    • Protein or peptide: Flagellar M-ring protein
KeywordsIn situ cryo-EM / sheathed flagellar motor / Vibrio cholerae / MS-ring / FliF / assembled state / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body, MS ring / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / plasma membrane
Similarity search - Function
Flagellar M-ring protein FliF / Flagellar M-ring C-terminal / Flagellar M-ring protein C-terminal / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Flagellar M-ring protein
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsGuo W / Yue J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI087946 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI132818 United States
CitationJournal: To Be Published
Title: In-situ cryo-EM structures reveal mechanisms of sheathed flagellar assembly, rotation, and disassembly in Vibrio cholerae
Authors: Wangbiao G / Jian Y / Jin HP / Fitnat Y / Jun L
History
DepositionSep 23, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72840.png

Downloads & links

-
Map

FileDownload / File: emd_72840.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRBM3 of FliF protin in MSring of flagellar motor in Vibrio cholerae.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 448 pix.
= 640.64 Å		1.43 Å/pix.
x 448 pix.
= 640.64 Å		1.43 Å/pix.
x 448 pix.
= 640.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.43 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.2492555 - 1.4769322
Average (Standard dev.)0.00068421033 (±0.022290546)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 640.63995 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_72840_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: RBM3 of FliF protin in MSring of flagellar motor in Vibrio cholerae.

Fileemd_72840_half_map_1.map
AnnotationRBM3 of FliF protin in MSring of flagellar motor in Vibrio cholerae.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: RBM3 of FliF protin in MSring of flagellar motor in Vibrio cholerae.

Fileemd_72840_half_map_2.map
AnnotationRBM3 of FliF protin in MSring of flagellar motor in Vibrio cholerae.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Vibrio cholerae

EntireName: Vibrio cholerae (bacteria)
Components
  • Cell: Vibrio cholerae
    • Protein or peptide: Flagellar M-ring protein

-
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)

-
Macromolecule #1: Flagellar M-ring protein

MacromoleculeName: Flagellar M-ring protein / type: protein_or_peptide / ID: 1 / Number of copies: 34 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 21.495785 KDa
SequenceString: VSAARRKEQE LEKQQEEALR GKIDSVLIPI LGLGNYTAQV DIELDFSAVE QTRKVFDPNT PATRSEYTLE DYNNGNVVAG VPGALSNQP PADASIPQDV AQMKDGSVMG QGSVHKEATR NYELDTTISH ERKQSGVINR QTVAVAVKSR SSVNPDTGEV T YTPLSEAD ...String:
VSAARRKEQE LEKQQEEALR GKIDSVLIPI LGLGNYTAQV DIELDFSAVE QTRKVFDPNT PATRSEYTLE DYNNGNVVAG VPGALSNQP PADASIPQDV AQMKDGSVMG QGSVHKEATR NYELDTTISH ERKQSGVINR QTVAVAVKSR SSVNPDTGEV T YTPLSEAD LNSIRQVLIG TVGYSENRGD LLNVLSMPFA

UniProtKB: Flagellar M-ring protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C34 (34 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 44428
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more