[English] 日本語
Yorodumi
- EMDB-72849: Rod-hook protein in Vibrio cholerae at assembled, opened state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72849
TitleRod-hook protein in Vibrio cholerae at assembled, opened state
Map data
Sample
  • Cell: Vibrio cholerae
    • Protein or peptide: Flagellar basal-body rod protein FlgG
    • Protein or peptide: Flagellar basal-body rod protein FlgF
    • Protein or peptide: Flagellar hook protein FlgE
KeywordsIn situ cryo-EM / sheathed flagellar motor / Vibrio cholerae / rod-hook / assembled state / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum hook / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / cytosol
Similarity search - Function
Flagellar basal-body rod FlgF / Flagellar basal-body rod FlgG / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, conserved site ...Flagellar basal-body rod FlgF / Flagellar basal-body rod FlgG / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagellar basal-body/hook protein, C-terminal domain / Flagella basal body rod protein / Flagellar basal body rod FlgEFG protein C-terminal
Similarity search - Domain/homology
Flagellar hook protein FlgE / Flagellar basal-body rod protein FlgF / Flagellar basal-body rod protein FlgG
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 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 24, 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_72849.png

Downloads & links

-
Map

FileDownload / File: emd_72849.map.gz / Format: CCP4 / Size: 1000 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 Å/pix.
x 640 pix.
= 640. Å		1 Å/pix.
x 640 pix.
= 640. Å		1 Å/pix.
x 640 pix.
= 640. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.30571803 - 13.575782
Average (Standard dev.)0.02993019 (±0.39771584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 640.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_72849_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_72849_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Rod in Vibrio cholerae.

Fileemd_72849_half_map_1.map
AnnotationRod in Vibrio cholerae.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Rod in Vibrio cholerae.

Fileemd_72849_half_map_2.map
AnnotationRod 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 basal-body rod protein FlgG
    • Protein or peptide: Flagellar basal-body rod protein FlgF
    • Protein or peptide: Flagellar hook protein FlgE

-
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 basal-body rod protein FlgG

MacromoleculeName: Flagellar basal-body rod protein FlgG / type: protein_or_peptide / ID: 1 / Number of copies: 27 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 28.11435 KDa
SequenceString: MQPALWVSKT GLDAQQTNIA TISNNLANAS TIGFKKGRAV FEDLFYQNIN QPGAQSSQNT RLPSGLMLGA GSKVVATQKV HTNGNVQTT SNSLDMMIEG DGFFQILMPD GNIAYSRNGQ FTLDDEGAIV TSGAGYRLQP EIIIPEDAIS ITIGNDGEVS V RVRGQQDN ...String:
MQPALWVSKT GLDAQQTNIA TISNNLANAS TIGFKKGRAV FEDLFYQNIN QPGAQSSQNT RLPSGLMLGA GSKVVATQKV HTNGNVQTT SNSLDMMIEG DGFFQILMPD GNIAYSRNGQ FTLDDEGAIV TSGAGYRLQP EIIIPEDAIS ITIGNDGEVS V RVRGQQDN QVLGQITTVD FINPGGLEPV GQNLYLPTGA SGEPQEGVPG LDGLGDIRQS MLETSNVNVT EELVNMIEAQ RV YEMNSKV ISAVDKMMSF VNQQL

UniProtKB: Flagellar basal-body rod protein FlgG

-
Macromolecule #2: Flagellar basal-body rod protein FlgF

MacromoleculeName: Flagellar basal-body rod protein FlgF / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 26.77827 KDa
SequenceString: MDRALFLAMS GAKQNMQAMQ LRANNLANVS TTGFRADLAQ ARSMQAYGEG LPSRVFSMTE RPGHNFAQGS VITTGRDLDI TIQGDGWIS VLDKTGKEGL TRNGNLRIDE TGLLLNGNGH PVLGETGAPI TLPVPLNKVE IGGDGTISVR PQGAPADAME V VDRIKLVR ...String:
MDRALFLAMS GAKQNMQAMQ LRANNLANVS TTGFRADLAQ ARSMQAYGEG LPSRVFSMTE RPGHNFAQGS VITTGRDLDI TIQGDGWIS VLDKTGKEGL TRNGNLRIDE TGLLLNGNGH PVLGETGAPI TLPVPLNKVE IGGDGTISVR PQGAPADAME V VDRIKLVR LNDQSLFKDV NGLFRATDPN TQFEADASVK ILTGALEGSN VNAIGEMTSL IDLQRQFEMQ VKMMSTAEEM DK ASDSLLR SS

UniProtKB: Flagellar basal-body rod protein FlgF

-
Macromolecule #3: Flagellar hook protein FlgE

MacromoleculeName: Flagellar hook protein FlgE / type: protein_or_peptide / ID: 3 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 46.880289 KDa
SequenceString: MSYVSLSGLS AAQMDLNTTS NNIANANTFG FKESRAEFGD VYSTSLFTNA KTTPGQGVQA AKVAQQFHEG SSIYTNNPLD LRIAGTGFF AVAKDRLVPQ QNELTRNGAF HLDKNSFMVT ANDEFLLGYE VNPDTGDVLS YEPKPINIPP QFGKPKQTAN I DLGANLPA ...String:
MSYVSLSGLS AAQMDLNTTS NNIANANTFG FKESRAEFGD VYSTSLFTNA KTTPGQGVQA AKVAQQFHEG SSIYTNNPLD LRIAGTGFF AVAKDRLVPQ QNELTRNGAF HLDKNSFMVT ANDEFLLGYE VNPDTGDVLS YEPKPINIPP QFGKPKQTAN I DLGANLPA NGDLKDPALF DITDPETYNR TTSSTIYDSM GQPYKLTTYY LKDMNQANTW QTYYTVTDKT GEKPINVVGG DA ASPTGHV GHTMRFNNDG TLSSLNNGQP IVTEPLGGGA NPVDLNGADV NQTLSFSLDS ATQFAAPFEL TKFDQDGATT GFL TKIDFD ENGSVLATYS NGINTTLGRV ALVRVANEQG LDKKGGTQWD ATQFSGAKIW GESNKGSFGS ISNGSLEQSN IDMT QELVD LISAQRNFQA NSRALEVHNG LQQNILQIR

UniProtKB: Flagellar hook protein FlgE

-
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 77446
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