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- PDB-8yjt: Cryo-EM structure of the flagellar C ring in the CCW state -

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Basic information

Entry
Database: PDB / ID: 8yjt
TitleCryo-EM structure of the flagellar C ring in the CCW state
Components
  • 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


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 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: 5.9 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 CCW state
Authors: Tan, J.X. / Zhang, L. / Zhou, Y. / Zhu, Y.Q.
History
DepositionMar 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,136,767204
Polymers6,136,767204
Non-polymers00
Water00
1


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

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Components

#1: 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
#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 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

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: C ring-containing flagellar motor-hook complex in the CCW state
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMtris(hydroxymethyl)aminomethane hydrochlorideTris-HCl1
25 mMethylenediaminetetraacetic acidEDTA1
30.1 % v/voctylphenol ethoxylateTX-1001
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 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: 2 Blot force: -5 Wait time: 5 Blot total: 1 Drain time: 2

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Image recordingElectron dose: 41 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1.1particle selection
2EPUimage acquisition
4cryoSPARC4.1.1CTF correction
7UCSF Chimera1.17model fitting
8UCSF ChimeraX1.5model fitting
10cryoSPARC4.1.1initial Euler assignment
11cryoSPARC4.1.1final Euler assignment
13cryoSPARC4.1.13D reconstruction
14PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 19627 / Details: Particles were manually picked using cryoSPARC
SymmetryPoint symmetry: C34 (34 fold cyclic)
3D reconstructionResolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19627 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
ID 3D fitting-IDSource nameTypeAccession code
11AlphaFoldin silico model
21PDBexperimental model8XP0

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