[English] 日本語
Yorodumi
- PDB-8wiw: Cryo-EM structure of the flagellar C ring in the CW state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wiw
TitleCryo-EM structure of the flagellar C ring in the CW state
Components
  • Chemotaxis protein CheY
  • Flagellar M-ring protein
  • Flagellar motor switch protein FliG
  • Flagellar motor switch protein FliM
  • Flagellar motor switch protein FliN
KeywordsMOTOR PROTEIN / Flagellum / Flagellar motor / C ring / Switch complex
Function / homology
Function and homology information


archaeal or bacterial-type flagellum-dependent cell motility / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / phosphorelay signal transduction system / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / metal ion binding ...archaeal or bacterial-type flagellum-dependent cell motility / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / phosphorelay signal transduction system / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / metal ion binding / plasma membrane / cytoplasm
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 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily
Similarity search - Domain/homology
Flagellar motor switch protein FliG / Chemotaxis protein CheY / Flagellar M-ring protein / Flagellar motor switch protein FliM / Flagellar motor switch protein FliN
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsTan, J.X. / Zhang, L. / Zhou, Y. / Zhu, Y.Q.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81925024 China
National Natural Science Foundation of China (NSFC)U23A20163 China
Ministry of Science and Technology (MoST, China)2017YFA0503900 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the flagellar C ring in the CW state
Authors: Tan, J.X. / Zhang, L. / Zhou, Y. / Zhu, Y.Q.
History
DepositionSep 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: Flagellar motor switch protein FliN
C: Flagellar M-ring protein
S: Flagellar motor switch protein FliM
Z: Flagellar motor switch protein FliG
h: Chemotaxis protein CheY
o: Flagellar motor switch protein FliN
u: Flagellar motor switch protein FliN
AA: Flagellar motor switch protein FliN
D: Flagellar M-ring protein
T: Flagellar motor switch protein FliM
a: Flagellar motor switch protein FliG
i: Chemotaxis protein CheY
p: Flagellar motor switch protein FliN
v: Flagellar motor switch protein FliN
AB: Flagellar motor switch protein FliN
E: Flagellar M-ring protein
U: Flagellar motor switch protein FliM
b: Flagellar motor switch protein FliG
j: Chemotaxis protein CheY
q: Flagellar motor switch protein FliN
w: Flagellar motor switch protein FliN
AC: Flagellar motor switch protein FliN
F: Flagellar M-ring protein
V: Flagellar motor switch protein FliM
c: Flagellar motor switch protein FliG
k: Chemotaxis protein CheY
r: Flagellar motor switch protein FliN
x: Flagellar motor switch protein FliN
AD: Flagellar motor switch protein FliN
G: Flagellar M-ring protein
W: Flagellar motor switch protein FliM
d: Flagellar motor switch protein FliG
l: Chemotaxis protein CheY
s: Flagellar motor switch protein FliN
y: Flagellar motor switch protein FliN
AE: Flagellar motor switch protein FliN
H: Flagellar M-ring protein
X: Flagellar motor switch protein FliM
e: Flagellar motor switch protein FliG
m: Chemotaxis protein CheY
t: Flagellar motor switch protein FliN
z: Flagellar motor switch protein FliN
AF: Flagellar motor switch protein FliN
I: Flagellar M-ring protein
Y: Flagellar motor switch protein FliM
f: Flagellar motor switch protein FliG
n: Chemotaxis protein CheY
1: Flagellar motor switch protein FliN
2: Flagellar motor switch protein FliN
AG: Flagellar motor switch protein FliN
J: Flagellar M-ring protein
g: Flagellar motor switch protein FliM
3: Flagellar motor switch protein FliG
4: Chemotaxis protein CheY
5: Flagellar motor switch protein FliN
6: Flagellar motor switch protein FliN
AH: Flagellar motor switch protein FliN
K: Flagellar M-ring protein
7: Flagellar motor switch protein FliM
8: Flagellar motor switch protein FliG
9: Chemotaxis protein CheY
AI: Flagellar motor switch protein FliN
AJ: Flagellar motor switch protein FliN
AK: Flagellar motor switch protein FliN
L: Flagellar M-ring protein
AL: Flagellar motor switch protein FliM
AM: Flagellar motor switch protein FliG
AN: Chemotaxis protein CheY
AO: Flagellar motor switch protein FliN
AP: Flagellar motor switch protein FliN
AQ: Flagellar motor switch protein FliN
M: Flagellar M-ring protein
AR: Flagellar motor switch protein FliM
AS: Flagellar motor switch protein FliG
AT: Chemotaxis protein CheY
AU: Flagellar motor switch protein FliN
AV: Flagellar motor switch protein FliN
AW: Flagellar motor switch protein FliN
N: Flagellar M-ring protein
AX: Flagellar motor switch protein FliM
AY: Flagellar motor switch protein FliG
AZ: Chemotaxis protein CheY
Aa: Flagellar motor switch protein FliN
Ab: Flagellar motor switch protein FliN
Ac: Flagellar motor switch protein FliN
O: Flagellar M-ring protein
Ad: Flagellar motor switch protein FliM
Ae: Flagellar motor switch protein FliG
Af: Chemotaxis protein CheY
Ag: Flagellar motor switch protein FliN
Ah: Flagellar motor switch protein FliN
Ai: Flagellar motor switch protein FliN
P: Flagellar M-ring protein
Aj: Flagellar motor switch protein FliM
Ak: Flagellar motor switch protein FliG
Al: Chemotaxis protein CheY
Am: Flagellar motor switch protein FliN
An: Flagellar motor switch protein FliN
Ao: Flagellar motor switch protein FliN
Q: Flagellar M-ring protein
Ap: Flagellar motor switch protein FliM
Aq: Flagellar motor switch protein FliG
Ar: Chemotaxis protein CheY
As: Flagellar motor switch protein FliN
At: Flagellar motor switch protein FliN
Au: Flagellar motor switch protein FliN
R: Flagellar M-ring protein
Av: Flagellar motor switch protein FliM
Aw: Flagellar motor switch protein FliG
Ax: Chemotaxis protein CheY
Ay: Flagellar motor switch protein FliN
Az: Flagellar motor switch protein FliN
A1: Flagellar motor switch protein FliN
A2: Flagellar M-ring protein
A3: Flagellar motor switch protein FliM
A4: Flagellar motor switch protein FliG
A5: Chemotaxis protein CheY
A6: Flagellar motor switch protein FliN
A7: Flagellar motor switch protein FliN
A8: Flagellar motor switch protein FliN
A9: Flagellar M-ring protein
A0: Flagellar motor switch protein FliM
BA: Flagellar motor switch protein FliG
BB: Chemotaxis protein CheY
BC: Flagellar motor switch protein FliN
BD: Flagellar motor switch protein FliN
BE: Flagellar motor switch protein FliN
BF: Flagellar M-ring protein
BG: Flagellar motor switch protein FliM
BH: Flagellar motor switch protein FliG
BI: Chemotaxis protein CheY
BJ: Flagellar motor switch protein FliN
BK: Flagellar motor switch protein FliN
BL: Flagellar motor switch protein FliN
BM: Flagellar M-ring protein
BN: Flagellar motor switch protein FliM
BO: Flagellar motor switch protein FliG
BP: Chemotaxis protein CheY
BQ: Flagellar motor switch protein FliN
BR: Flagellar motor switch protein FliN
BS: Flagellar motor switch protein FliN
BT: Flagellar M-ring protein
BU: Flagellar motor switch protein FliM
BV: Flagellar motor switch protein FliG
BW: Chemotaxis protein CheY
BX: Flagellar motor switch protein FliN
BY: Flagellar motor switch protein FliN
BZ: Flagellar motor switch protein FliN
Ba: Flagellar M-ring protein
Bb: Flagellar motor switch protein FliM
Bc: Flagellar motor switch protein FliG
Bd: Chemotaxis protein CheY
Be: Flagellar motor switch protein FliN
Bf: Flagellar motor switch protein FliN
Bg: Flagellar motor switch protein FliN
Bh: Flagellar M-ring protein
Bi: Flagellar motor switch protein FliM
Bj: Flagellar motor switch protein FliG
Bk: Chemotaxis protein CheY
Bl: Flagellar motor switch protein FliN
Bm: Flagellar motor switch protein FliN
Bn: Flagellar motor switch protein FliN
Bo: Flagellar M-ring protein
Bp: Flagellar motor switch protein FliM
Bq: Flagellar motor switch protein FliG
Br: Chemotaxis protein CheY
Bs: Flagellar motor switch protein FliN
Bt: Flagellar motor switch protein FliN
Bu: Flagellar motor switch protein FliN
Bv: Flagellar M-ring protein
Bw: Flagellar motor switch protein FliM
Bx: Flagellar motor switch protein FliG
By: Chemotaxis protein CheY
Bz: Flagellar motor switch protein FliN
B1: Flagellar motor switch protein FliN
B2: Flagellar motor switch protein FliN
B3: Flagellar M-ring protein
B4: Flagellar motor switch protein FliM
B5: Flagellar motor switch protein FliG
B6: Chemotaxis protein CheY
B7: Flagellar motor switch protein FliN
B8: Flagellar motor switch protein FliN
B9: Flagellar motor switch protein FliN
B0: Flagellar M-ring protein
CA: Flagellar motor switch protein FliM
CB: Flagellar motor switch protein FliG
CC: Chemotaxis protein CheY
CD: Flagellar motor switch protein FliN
CE: Flagellar motor switch protein FliN
CF: Flagellar motor switch protein FliN
CG: Flagellar M-ring protein
CH: Flagellar motor switch protein FliM
CI: Flagellar motor switch protein FliG
CJ: Chemotaxis protein CheY
CK: Flagellar motor switch protein FliN
CL: Flagellar motor switch protein FliN
CM: Flagellar motor switch protein FliN
CN: Flagellar M-ring protein
CO: Flagellar motor switch protein FliM
CP: Flagellar motor switch protein FliG
CQ: Chemotaxis protein CheY
CR: Flagellar motor switch protein FliN
CS: Flagellar motor switch protein FliN
CT: Flagellar motor switch protein FliN
CU: Flagellar M-ring protein
CV: Flagellar motor switch protein FliM
CW: Flagellar motor switch protein FliG
CX: Chemotaxis protein CheY
CY: Flagellar motor switch protein FliN
CZ: Flagellar motor switch protein FliN
Ca: Flagellar motor switch protein FliN
Cb: Flagellar M-ring protein
Cc: Flagellar motor switch protein FliM
Cd: Flagellar motor switch protein FliG
Ce: Chemotaxis protein CheY
Cf: Flagellar motor switch protein FliN
Cg: Flagellar motor switch protein FliN
Ch: Flagellar motor switch protein FliN
Ci: Flagellar M-ring protein
Cj: Flagellar motor switch protein FliM
Ck: Flagellar motor switch protein FliG
Cl: Chemotaxis protein CheY
Cm: Flagellar motor switch protein FliN
Cn: Flagellar motor switch protein FliN
Co: Flagellar motor switch protein FliN
Cp: Flagellar M-ring protein
Cq: Flagellar motor switch protein FliM
Cr: Flagellar motor switch protein FliG
Cs: Chemotaxis protein CheY
Ct: Flagellar motor switch protein FliN
Cu: Flagellar motor switch protein FliN
Cv: Flagellar motor switch protein FliN
Cw: Flagellar M-ring protein
Cx: Flagellar motor switch protein FliM
Cy: Flagellar motor switch protein FliG
Cz: Chemotaxis protein CheY
C1: Flagellar motor switch protein FliN
C2: Flagellar motor switch protein FliN


Theoretical massNumber of molelcules
Total (without water)6,618,802238
Polymers6,618,802238
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein ...
Flagellar motor switch protein FliN


Mass: 14801.823 Da / Num. of mol.: 102 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P26419
#2: Protein ...
Flagellar M-ring protein


Mass: 61295.645 Da / Num. of mol.: 34 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P15928
#3: Protein ...
Flagellar motor switch protein FliM


Mass: 37901.066 Da / Num. of mol.: 34 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P26418
#4: Protein ...
Flagellar motor switch protein FliG


Mass: 36890.957 Da / Num. of mol.: 34 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P0A1J9
#5: Protein ...
Chemotaxis protein CheY


Mass: 14177.512 Da / Num. of mol.: 34 / Mutation: D13K, Y106W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Gene: cheY, STM1916 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A2D5

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: C ring-containing flagellar motor-hook complex in the CW state
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
111.7 mMtris(hydroxymethyl)aminomethane hydrochlorideTris-HCl1
24.17 mMethylenediaminetetraacetic acidEDTA1
30.083 % (v/v)octylphenol ethoxylateTX-1001
425 mMsodium chlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: This sample was prepared by incubating the C ring-containing flagellar motor-hook complex with the constitutively active mutant of CheY (CheY**)
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: Blot time: 4 Blot force: 10 Wait time: 30 Blot total: 1 Drain time: 2

-
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 magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1.1particle selection
2EPUimage acquisition
4cryoSPARC4.1.1CTF correction
7UCSF Chimera1.17model fitting
8UCSF ChimeraX1.5model fitting
9Coot0.9.8.7model fitting
11cryoSPARC4.1.1initial Euler assignment
12cryoSPARC4.1.1final Euler assignment
14cryoSPARC4.1.13D reconstruction
15PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 46058 / Details: Particles were manually picked using cryoSPARC
SymmetryPoint symmetry: C34 (34 fold cyclic)
3D reconstructionResolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28119 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 8XP1

8xp1


Accession code: 8XP1 / Source name: PDB / Type: experimental model

+
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://pdbjlvh1.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