[English] 日本語
Yorodumi
- EMDB-41100: CCW Flagellar Switch Complex - FliF, FliG, FliM, and FliN forming... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41100
TitleCCW Flagellar Switch Complex - FliF, FliG, FliM, and FliN forming 34-mer C-ring from Salmonella
Map data
Sample
  • Complex: Flagellar MS-ring and C-ring complex containing FliF, FliG, FliM, and FliN
    • Protein or peptide: Flagellar M-ring protein
    • Protein or peptide: Flagellar motor switch protein FliG
    • Protein or peptide: FliM,Flagellar motor switch protein FliM
    • Protein or peptide: Flagellar motor switch protein FliN
KeywordsDomain Swap / Symmetry mismatch / Flagellar component / Switch complex / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / plasma membrane
Similarity search - Function
Flagellar motor switch protein FliN, N-terminal / Flagellar motor switch protein FliN N-terminal / : / Flagellar motor switch FliN / Flagellar motor switch FliN/Type III secretion HrcQb / Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / Flagellar motor switch protein FliG / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal ...Flagellar motor switch protein FliN, N-terminal / Flagellar motor switch protein FliN N-terminal / : / Flagellar motor switch FliN / Flagellar motor switch FliN/Type III secretion HrcQb / Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / Flagellar motor switch protein FliG / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal / Flagellar motor switch protein FliG, N-terminal domain / Flagellar motor switch protein FliG, middle domain / FliG C-terminal domain / FliG middle domain / FliG N-terminal domain / CheC-like superfamily / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / 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 motor switch protein FliM / Flagellar motor switch protein FliN / Flagellar motor switch protein FliG / Flagellar motor switch protein FliG / Flagellar M-ring protein / Flagellar motor switch protein FliM / Flagellar motor switch protein FliN
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsSingh PK / Iverson TM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/John E. Fogarty International Center (NIH/FIC)GM61606 United States
CitationJournal: Nat Microbiol / Year: 2024
Title: CryoEM structures reveal how the bacterial flagellum rotates and switches direction.
Authors: Prashant K Singh / Pankaj Sharma / Oshri Afanzar / Margo H Goldfarb / Elena Maklashina / Michael Eisenbach / Gary Cecchini / T M Iverson /
Abstract: Bacterial chemotaxis requires bidirectional flagellar rotation at different rates. Rotation is driven by a flagellar motor, which is a supercomplex containing multiple rings. Architectural ...Bacterial chemotaxis requires bidirectional flagellar rotation at different rates. Rotation is driven by a flagellar motor, which is a supercomplex containing multiple rings. Architectural uncertainty regarding the cytoplasmic C-ring, or 'switch', limits our understanding of how the motor transmits torque and direction to the flagellar rod. Here we report cryogenic electron microscopy structures for Salmonella enterica serovar typhimurium inner membrane MS-ring and C-ring in a counterclockwise pose (4.0 Å) and isolated C-ring in a clockwise pose alone (4.6 Å) and bound to a regulator (5.9 Å). Conformational differences between rotational poses include a 180° shift in FliF/FliG domains that rotates the outward-facing MotA/B binding site to inward facing. The regulator has specificity for the clockwise pose by bridging elements unique to this conformation. We used these structures to propose how the switch reverses rotation and transmits torque to the flagellum, which advances the understanding of bacterial chemotaxis and bidirectional motor rotation.
History
DepositionJun 22, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41100.png

Downloads & links

-
Map

FileDownload / File: emd_41100.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 768 pix.
= 1046.784 Å		1.36 Å/pix.
x 768 pix.
= 1046.784 Å		1.36 Å/pix.
x 768 pix.
= 1046.784 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.363 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.147
Minimum - Maximum-0.13342229 - 0.4831149
Average (Standard dev.)-0.00086792343 (±0.015738653)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 1046.784 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_41100_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_41100_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_41100_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Flagellar MS-ring and C-ring complex containing FliF, FliG, FliM,...

EntireName: Flagellar MS-ring and C-ring complex containing FliF, FliG, FliM, and FliN
Components
  • Complex: Flagellar MS-ring and C-ring complex containing FliF, FliG, FliM, and FliN
    • Protein or peptide: Flagellar M-ring protein
    • Protein or peptide: Flagellar motor switch protein FliG
    • Protein or peptide: FliM,Flagellar motor switch protein FliM
    • Protein or peptide: Flagellar motor switch protein FliN

-
Supramolecule #1: Flagellar MS-ring and C-ring complex containing FliF, FliG, FliM,...

SupramoleculeName: Flagellar MS-ring and C-ring complex containing FliF, FliG, FliM, and FliN
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 3.5 MDa

-
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: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 5.644328 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
KDEQLQQRRA NQRLGAEVMS QRIREMSDND PRVVALVIRQ WMSNDHE

UniProtKB: Flagellar M-ring protein

-
Macromolecule #2: Flagellar motor switch protein FliG

MacromoleculeName: Flagellar motor switch protein FliG / type: protein_or_peptide / ID: 2 / Number of copies: 34 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 36.890957 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSNLSGTDKS VILLMTIGED RAAEVFKHLS TREVQALSTA MANVRQISNK QLTDVLSEFE QEAEQFAALN INANEYLRSV LVKALGEER ASSLLEDILE TRDTTSGIET LNFMEPQSAA DLIRDEHPQI IATILVHLKR SQAADILALF DERLRHDVML R IATFGGVQ ...String:
MSNLSGTDKS VILLMTIGED RAAEVFKHLS TREVQALSTA MANVRQISNK QLTDVLSEFE QEAEQFAALN INANEYLRSV LVKALGEER ASSLLEDILE TRDTTSGIET LNFMEPQSAA DLIRDEHPQI IATILVHLKR SQAADILALF DERLRHDVML R IATFGGVQ PAALAELTEV LNGLLDGQNL KRSKMGGVRT AAEIINLMKT QQEEAVITAV REFDGELAQK IIDEMFLFEN LV DVDDRSI QRLLQEVDSE SLLIALKGAE PPLREKFLRN MSQRAADILR DDLANRGPVR LSQVENEQKA ILLIVRRLAE TGE MVIGSG EDTYV

UniProtKB: Flagellar motor switch protein FliG

-
Macromolecule #3: FliM,Flagellar motor switch protein FliM

MacromoleculeName: FliM,Flagellar motor switch protein FliM / type: protein_or_peptide / ID: 3 / Number of copies: 34 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 33.758836 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) LQA LEIINERFAR QFRMGLFNLL RRSPDITVGA IRIQPYHEFA RNLPVPTNLN LIHLKPLRGT GLVVFSPSLV FIAVDNL FG GDGRFPTKVE ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) LQA LEIINERFAR QFRMGLFNLL RRSPDITVGA IRIQPYHEFA RNLPVPTNLN LIHLKPLRGT GLVVFSPSLV FIAVDNL FG GDGRFPTKVE GREFTHTEQR VINRMLKLAL EGYSDAWKAI NPLEVEYVRS EMQVKFTNIT TSPNDIVVNT PFHVEIGN L TGEFNICLPF SMIEPLRELL VNPPLENSRH EDQNWRDNLV RQVQHSELEL VANFADIPLR LSQILKLKPG DVLPIEKPD RIIAHVDGVP VLTSQYGTVN GQYALRVEHL INPILNSLNE EQPK

UniProtKB: Flagellar motor switch protein FliM

-
Macromolecule #4: Flagellar motor switch protein FliN

MacromoleculeName: Flagellar motor switch protein FliN / type: protein_or_peptide / ID: 4 / Number of copies: 102 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 14.801823 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSDMNNPSDE NTGALDDLWA DALNEQKATT TKSAADAVFQ QLGGGDVSGA MQDIDLIMDI PVKLTVELGR TRMTIKELLR LTQGSVVAL DGLAGEPLDI LINGYLIAQG EVVVVADKYG VRITDIITPS ERMRRLSR

UniProtKB: Flagellar motor switch protein FliN

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.557 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER / Details: Ab-initio model
Final reconstructionApplied symmetry - Point group: C34 (34 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 51268
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
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