[English] 日本語
Yorodumi
- EMDB-49131: In situ sheathed flagellar FlaC filament in Vibrio cholerae. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49131
TitleIn situ sheathed flagellar FlaC filament in Vibrio cholerae.
Map dataIn situ sheathed flagellar filament of DflhGDflaBDE Vibrio cholerae.
Sample
  • Complex: Sheathed flagellar filament in DflhGDflaBDE Vibrio cholerae.
    • Protein or peptide: Flagellin C
KeywordsIn situ cryo-EM / sheathed flagellar filament / FlaC / 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: 3.16 Å
AuthorsWangbiao G / Rajeev K
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

-
Structure visualization

Supplemental images

emd_49131.png

Downloads & links

-
Map

FileDownload / File: emd_49131.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn situ sheathed flagellar filament of DflhGDflaBDE 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: 0.14
Minimum - Maximum-0.23918957 - 0.4797685
Average (Standard dev.)0.005503846 (±0.026686389)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_49131_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: In situ sheathed flagellar filament of DflhGDflaBDE Vibrio cholerae.

Fileemd_49131_half_map_1.map
AnnotationIn situ sheathed flagellar filament of DflhGDflaBDE Vibrio cholerae.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: In situ sheathed flagellar filament of DflhGDflaBDE Vibrio cholerae.

Fileemd_49131_half_map_2.map
AnnotationIn situ sheathed flagellar filament of DflhGDflaBDE Vibrio cholerae.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Sheathed flagellar filament in DflhGDflaBDE Vibrio cholerae.

EntireName: Sheathed flagellar filament in DflhGDflaBDE Vibrio cholerae.
Components
  • Complex: Sheathed flagellar filament in DflhGDflaBDE Vibrio cholerae.
    • Protein or peptide: Flagellin C

-
Supramolecule #1: Sheathed flagellar filament in DflhGDflaBDE Vibrio cholerae.

SupramoleculeName: Sheathed flagellar filament in DflhGDflaBDE Vibrio cholerae.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: In situ sheathed flagellar filament of DflhGDflaBDE Vibrio cholerae.
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)

-
Macromolecule #1: Flagellin C

MacromoleculeName: Flagellin C / 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: 39.944117 KDa
SequenceString: MAVNVNTNVS AMTAQRYLTS ATNAQQSSME RLSSGYKINS AKDDAAGLQI SNRLNVQSRG LGVAVRNAND GISMAQTAEG AMKETTNIL QRMRDLSLQS ANGSNSKADR VAIQEEITAL NDELNRVAET TSFGGNKLLN GTFATKSFQI GADNGEAVML N IKDMRSDN ...String:
MAVNVNTNVS AMTAQRYLTS ATNAQQSSME RLSSGYKINS AKDDAAGLQI SNRLNVQSRG LGVAVRNAND GISMAQTAEG AMKETTNIL QRMRDLSLQS ANGSNSKADR VAIQEEITAL NDELNRVAET TSFGGNKLLN GTFATKSFQI GADNGEAVML N IKDMRSDN ALMGGKTYQA ANGKDKNWGV EAGKTDLTIT LKDKREGDVT ISINAKEGDD IEELATYING QTDMIKASVD EE GKLQLFT DNNRIDGAAT FGGALAGELG IGAAQDVTVD TLDVTTVGGA QESVAIVDAA LKYVDSHRAE LGAFQNRFNH AIN NLDNIN ENVNASKSRI KDTDFAKETT ALTKAQILSQ ASSSVLAQAK QAPNSALALL G

UniProtKB: Flagellin C

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 300613
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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