[English] 日本語
Yorodumi
- PDB-8vkq: CW Flagellar Switch Complex - FliF, FliG, FliM, and FliN forming ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vkq
TitleCW Flagellar Switch Complex - FliF, FliG, FliM, and FliN forming the C-ring from Salmonella
Components
  • Flagellar M-ring protein
  • Flagellar motor switch protein FliG
  • Flagellar motor switch protein FliM
  • Flagellar motor switch protein FliN
KeywordsMOTOR PROTEIN / Domain Swap / Symmetry mismatch / Flagellar component / Switch complex
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 FliG / Flagellar motor switch protein FliM / Flagellar M-ring protein / Flagellar motor switch protein FliN
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsSingh, P.K. / Iverson, T.M.
Funding support United States, 1items
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
DepositionJan 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: pdbx_database_related
Revision 1.2Aug 21, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: Flagellar M-ring protein
G: Flagellar motor switch protein FliG
M: Flagellar motor switch protein FliM
N: Flagellar motor switch protein FliN
P: Flagellar motor switch protein FliN
Q: Flagellar motor switch protein FliN
A: Flagellar M-ring protein
B: Flagellar motor switch protein FliG
C: Flagellar motor switch protein FliM
D: Flagellar motor switch protein FliN
E: Flagellar motor switch protein FliN
H: Flagellar motor switch protein FliN
I: Flagellar M-ring protein
J: Flagellar motor switch protein FliG
K: Flagellar motor switch protein FliM
L: Flagellar motor switch protein FliN
O: Flagellar motor switch protein FliN
R: Flagellar motor switch protein FliN
S: Flagellar M-ring protein
T: Flagellar motor switch protein FliG
V: Flagellar motor switch protein FliM
W: Flagellar motor switch protein FliN
X: Flagellar motor switch protein FliN
Y: Flagellar motor switch protein FliN
Z: Flagellar M-ring protein
AA: Flagellar motor switch protein FliG
BA: Flagellar motor switch protein FliM
CA: Flagellar motor switch protein FliN
DA: Flagellar motor switch protein FliN
EA: Flagellar motor switch protein FliN
FA: Flagellar M-ring protein
GA: Flagellar motor switch protein FliG
HA: Flagellar motor switch protein FliM
IA: Flagellar motor switch protein FliN
JA: Flagellar motor switch protein FliN
KA: Flagellar motor switch protein FliN
LA: Flagellar M-ring protein
MA: Flagellar motor switch protein FliG
NA: Flagellar motor switch protein FliM
OA: Flagellar motor switch protein FliN
PA: Flagellar motor switch protein FliN
QA: Flagellar motor switch protein FliN
RA: Flagellar M-ring protein
SA: Flagellar motor switch protein FliG
TA: Flagellar motor switch protein FliM
UA: Flagellar motor switch protein FliN
VA: Flagellar motor switch protein FliN
WA: Flagellar motor switch protein FliN
XA: Flagellar M-ring protein
YA: Flagellar motor switch protein FliG
ZA: Flagellar motor switch protein FliM
AB: Flagellar motor switch protein FliN
BB: Flagellar motor switch protein FliN
CB: Flagellar motor switch protein FliN
DB: Flagellar M-ring protein
EB: Flagellar motor switch protein FliG
FB: Flagellar motor switch protein FliM
GB: Flagellar motor switch protein FliN
HB: Flagellar motor switch protein FliN
IB: Flagellar motor switch protein FliN
JB: Flagellar M-ring protein
KB: Flagellar motor switch protein FliG
LB: Flagellar motor switch protein FliM
MB: Flagellar motor switch protein FliN
NB: Flagellar motor switch protein FliN
OB: Flagellar motor switch protein FliN
PB: Flagellar M-ring protein
QB: Flagellar motor switch protein FliG
RB: Flagellar motor switch protein FliM
SB: Flagellar motor switch protein FliN
TB: Flagellar motor switch protein FliN
UB: Flagellar motor switch protein FliN
VB: Flagellar M-ring protein
WB: Flagellar motor switch protein FliG
XB: Flagellar motor switch protein FliM
YB: Flagellar motor switch protein FliN
ZB: Flagellar motor switch protein FliN
AC: Flagellar motor switch protein FliN
BC: Flagellar M-ring protein
CC: Flagellar motor switch protein FliG
DC: Flagellar motor switch protein FliM
EC: Flagellar motor switch protein FliN
FC: Flagellar motor switch protein FliN
GC: Flagellar motor switch protein FliN
HC: Flagellar M-ring protein
IC: Flagellar motor switch protein FliG
JC: Flagellar motor switch protein FliM
KC: Flagellar motor switch protein FliN
LC: Flagellar motor switch protein FliN
MC: Flagellar motor switch protein FliN
NC: Flagellar M-ring protein
OC: Flagellar motor switch protein FliG
PC: Flagellar motor switch protein FliM
QC: Flagellar motor switch protein FliN
RC: Flagellar motor switch protein FliN
SC: Flagellar motor switch protein FliN
TC: Flagellar M-ring protein
UC: Flagellar motor switch protein FliG
VC: Flagellar motor switch protein FliM
WC: Flagellar motor switch protein FliN
XC: Flagellar motor switch protein FliN
YC: Flagellar motor switch protein FliN
ZC: Flagellar M-ring protein
AD: Flagellar motor switch protein FliG
BD: Flagellar motor switch protein FliM
CD: Flagellar motor switch protein FliN
DD: Flagellar motor switch protein FliN
ED: Flagellar motor switch protein FliN
FD: Flagellar M-ring protein
GD: Flagellar motor switch protein FliG
HD: Flagellar motor switch protein FliM
ID: Flagellar motor switch protein FliN
JD: Flagellar motor switch protein FliN
KD: Flagellar motor switch protein FliN
LD: Flagellar M-ring protein
MD: Flagellar motor switch protein FliG
ND: Flagellar motor switch protein FliM
OD: Flagellar motor switch protein FliN
PD: Flagellar motor switch protein FliN
QD: Flagellar motor switch protein FliN
RD: Flagellar M-ring protein
SD: Flagellar motor switch protein FliG
TD: Flagellar motor switch protein FliM
UD: Flagellar motor switch protein FliN
VD: Flagellar motor switch protein FliN
WD: Flagellar motor switch protein FliN
XD: Flagellar M-ring protein
YD: Flagellar motor switch protein FliG
ZD: Flagellar motor switch protein FliM
AE: Flagellar motor switch protein FliN
BE: Flagellar motor switch protein FliN
CE: Flagellar motor switch protein FliN
DE: Flagellar M-ring protein
EE: Flagellar motor switch protein FliG
FE: Flagellar motor switch protein FliM
GE: Flagellar motor switch protein FliN
HE: Flagellar motor switch protein FliN
IE: Flagellar motor switch protein FliN
JE: Flagellar M-ring protein
KE: Flagellar motor switch protein FliG
LE: Flagellar motor switch protein FliM
ME: Flagellar motor switch protein FliN
NE: Flagellar motor switch protein FliN
OE: Flagellar motor switch protein FliN
PE: Flagellar M-ring protein
QE: Flagellar motor switch protein FliG
RE: Flagellar motor switch protein FliM
SE: Flagellar motor switch protein FliN
TE: Flagellar motor switch protein FliN
UE: Flagellar motor switch protein FliN
VE: Flagellar M-ring protein
WE: Flagellar motor switch protein FliG
XE: Flagellar motor switch protein FliM
YE: Flagellar motor switch protein FliN
ZE: Flagellar motor switch protein FliN
AF: Flagellar motor switch protein FliN
BF: Flagellar M-ring protein
CF: Flagellar motor switch protein FliG
DF: Flagellar motor switch protein FliM
EF: Flagellar motor switch protein FliN
FF: Flagellar motor switch protein FliN
GF: Flagellar motor switch protein FliN
HF: Flagellar M-ring protein
IF: Flagellar motor switch protein FliG
JF: Flagellar motor switch protein FliM
KF: Flagellar motor switch protein FliN
LF: Flagellar motor switch protein FliN
MF: Flagellar motor switch protein FliN
NF: Flagellar M-ring protein
OF: Flagellar motor switch protein FliG
PF: Flagellar motor switch protein FliM
QF: Flagellar motor switch protein FliN
RF: Flagellar motor switch protein FliN
SF: Flagellar motor switch protein FliN
TF: Flagellar M-ring protein
UF: Flagellar motor switch protein FliG
VF: Flagellar motor switch protein FliM
WF: Flagellar motor switch protein FliN
XF: Flagellar motor switch protein FliN
YF: Flagellar motor switch protein FliN
ZF: Flagellar M-ring protein
AG: Flagellar motor switch protein FliG
BG: Flagellar motor switch protein FliM
CG: Flagellar motor switch protein FliN
DG: Flagellar motor switch protein FliN
EG: Flagellar motor switch protein FliN
FG: Flagellar M-ring protein
GG: Flagellar motor switch protein FliG
HG: Flagellar motor switch protein FliM
IG: Flagellar motor switch protein FliN
JG: Flagellar motor switch protein FliN
KG: Flagellar motor switch protein FliN
LG: Flagellar M-ring protein
MG: Flagellar motor switch protein FliG
NG: Flagellar motor switch protein FliM
OG: Flagellar motor switch protein FliN
PG: Flagellar motor switch protein FliN
QG: Flagellar motor switch protein FliN
RG: Flagellar M-ring protein
SG: Flagellar motor switch protein FliG
TG: Flagellar motor switch protein FliM
UG: Flagellar motor switch protein FliN
VG: Flagellar motor switch protein FliN
WG: Flagellar motor switch protein FliN


Theoretical massNumber of molelcules
Total (without water)5,968,868204
Polymers5,968,868204
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein ...
Flagellar M-ring protein / FliF


Mass: 61295.645 Da / Num. of mol.: 34
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: fliF, fla AII.1, fla BI, STM1969 / Production host: Escherichia coli (E. coli) / References: UniProt: P15928
#2: Protein ...
Flagellar motor switch protein FliG


Mass: 36860.930 Da / Num. of mol.: 34
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: fliG, AUA10_01480, AUA59_00550 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5W0I7H9
#3: Protein ...
Flagellar motor switch protein FliM


Mass: 32992.895 Da / Num. of mol.: 34
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: fliM, G0L96_06560 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5Y0LQY3
#4: Protein ...
Flagellar motor switch protein FliN


Mass: 14801.823 Da / Num. of mol.: 102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: fliN, flaN, motD, STM1977 / Production host: Escherichia coli (E. coli) / References: UniProt: P26419

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Flagellar C-ring containing FliF, FliG, FliM, and FliN
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 3.5 MDa / Experimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 56.323 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategoryDetails
4cryoSPARC4.2.1CTF correction
10cryoSPARC4.2.1initial Euler assignment
11cryoSPARC4.2.1final Euler assignment
12cryoSPARC4.2.1classification
13cryoSPARC4.2.13D reconstructionTo perform refinement and local refinement
14RELION4.0.13D reconstructionrelion_image_handler to build the ring
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7201 / Symmetry type: POINT

+
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