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- PDB-8wkk: Cryo-EM structure of the whole rod with export apparatus and hook... -

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Basic information

Entry
Database: PDB / ID: 8wkk
TitleCryo-EM structure of the whole rod with export apparatus and hook within the flagellar motor-hook complex in the CW state.
Components
  • (Flagellar basal-body rod protein ...) x 3
  • (Flagellar biosynthetic protein ...) x 3
  • Flagellar M-ring protein
  • Flagellar basal body rod protein FlgB
  • Flagellar hook protein FlgE
  • Flagellar hook-basal body complex protein FliE
KeywordsMOTOR PROTEIN / Flagellum / Flagellar motor
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum organization / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / cytoskeletal motor activity / protein secretion / bacterial-type flagellum-dependent cell motility ...bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum organization / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / cytoskeletal motor activity / protein secretion / bacterial-type flagellum-dependent cell motility / protein targeting / structural molecule activity / plasma membrane
Similarity search - Function
Flagellar basal-body rod protein FlgC / Flagellar basal-body rod FlgG / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar biosynthesis protein FliQ / Flagellar biosynthesis protein FliR / Flagellar transport protein FliP / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE ...Flagellar basal-body rod protein FlgC / Flagellar basal-body rod FlgG / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar biosynthesis protein FliQ / Flagellar biosynthesis protein FliR / Flagellar transport protein FliP / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / Type III secretion system inner membrane R protein / Bacterial export protein family 3 / Bacterial export proteins, family 1 / Bacterial export proteins, family 3 / Flagella transport protein fliP family signature 1. / Type III secretion system inner membrane P protein / FliP family / Flagella transport protein fliP family signature 2. / 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 / 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 basal-body rod protein FlgC / Flagellar hook protein FlgE / Flagellar basal-body rod protein FlgG / Flagellar biosynthetic protein FliQ / Flagellar M-ring protein / Flagellar basal-body rod protein FlgF / Flagellar basal body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar biosynthetic protein FliP / Flagellar biosynthetic protein FliR
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 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 whole rod with export apparatus and hook within the flagellar motor-hook complex in the CW state.
Authors: Tan, J.X. / Zhang, L. / Zhou, Y. / Zhu, Y.Q.
History
DepositionSep 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellar biosynthetic protein FliQ
B: Flagellar biosynthetic protein FliQ
C: Flagellar biosynthetic protein FliQ
D: Flagellar biosynthetic protein FliQ
E: Flagellar biosynthetic protein FliR
F: Flagellar biosynthetic protein FliP
G: Flagellar biosynthetic protein FliP
H: Flagellar biosynthetic protein FliP
I: Flagellar biosynthetic protein FliP
J: Flagellar biosynthetic protein FliP
K: Flagellar hook-basal body complex protein FliE
L: Flagellar hook-basal body complex protein FliE
M: Flagellar hook-basal body complex protein FliE
N: Flagellar hook-basal body complex protein FliE
O: Flagellar hook-basal body complex protein FliE
P: Flagellar hook-basal body complex protein FliE
Q: Flagellar basal body rod protein FlgB
R: Flagellar basal body rod protein FlgB
S: Flagellar basal body rod protein FlgB
T: Flagellar basal body rod protein FlgB
U: Flagellar basal body rod protein FlgB
V: Flagellar basal-body rod protein FlgC
W: Flagellar basal-body rod protein FlgC
X: Flagellar basal-body rod protein FlgC
Y: Flagellar basal-body rod protein FlgC
Z: Flagellar basal-body rod protein FlgC
a: Flagellar basal-body rod protein FlgC
b: Flagellar M-ring protein
c: Flagellar M-ring protein
d: Flagellar M-ring protein
e: Flagellar M-ring protein
f: Flagellar M-ring protein
g: Flagellar M-ring protein
h: Flagellar M-ring protein
i: Flagellar M-ring protein
j: Flagellar M-ring protein
k: Flagellar M-ring protein
l: Flagellar M-ring protein
m: Flagellar basal-body rod protein FlgF
n: Flagellar basal-body rod protein FlgF
o: Flagellar basal-body rod protein FlgF
p: Flagellar basal-body rod protein FlgF
q: Flagellar basal-body rod protein FlgF
0: Flagellar basal-body rod protein FlgG
1: Flagellar basal-body rod protein FlgG
2: Flagellar basal-body rod protein FlgG
3: Flagellar basal-body rod protein FlgG
4: Flagellar basal-body rod protein FlgG
5: Flagellar basal-body rod protein FlgG
6: Flagellar basal-body rod protein FlgG
7: Flagellar basal-body rod protein FlgG
8: Flagellar basal-body rod protein FlgG
9: Flagellar basal-body rod protein FlgG
ZA: Flagellar basal-body rod protein FlgG
ZB: Flagellar basal-body rod protein FlgG
ZC: Flagellar basal-body rod protein FlgG
ZD: Flagellar basal-body rod protein FlgG
ZE: Flagellar basal-body rod protein FlgG
ZF: Flagellar hook protein FlgE
ZG: Flagellar hook protein FlgE
ZH: Flagellar hook protein FlgE
ZI: Flagellar hook protein FlgE
ZJ: Flagellar hook protein FlgE
ZK: Flagellar hook protein FlgE
ZL: Flagellar hook protein FlgE
ZM: Flagellar hook protein FlgE
ZN: Flagellar hook protein FlgE
ZO: Flagellar hook protein FlgE
ZP: Flagellar hook protein FlgE
ZQ: Flagellar hook protein FlgE
ZR: Flagellar hook protein FlgE
ZS: Flagellar hook protein FlgE
ZT: Flagellar hook protein FlgE
ZU: Flagellar hook protein FlgE
ZV: Flagellar hook protein FlgE
ZW: Flagellar hook protein FlgE
ZX: Flagellar hook protein FlgE
ZY: Flagellar hook protein FlgE
ZZ: Flagellar hook protein FlgE
Za: Flagellar hook protein FlgE
Zb: Flagellar hook protein FlgE
Zc: Flagellar hook protein FlgE
Zd: Flagellar hook protein FlgE
Ze: Flagellar hook protein FlgE
Zf: Flagellar hook protein FlgE
Zg: Flagellar hook protein FlgE
Zh: Flagellar hook protein FlgE
r: Flagellar basal-body rod protein FlgG
s: Flagellar basal-body rod protein FlgG
t: Flagellar basal-body rod protein FlgG
u: Flagellar basal-body rod protein FlgG
v: Flagellar basal-body rod protein FlgG
w: Flagellar basal-body rod protein FlgG
x: Flagellar basal-body rod protein FlgG
y: Flagellar basal-body rod protein FlgG
z: Flagellar basal-body rod protein FlgG


Theoretical massNumber of molelcules
Total (without water)3,124,02996
Polymers3,124,02996
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

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Flagellar biosynthetic protein ... , 3 types, 10 molecules ABCDEFGHIJ

#1: Protein
Flagellar biosynthetic protein FliQ


Mass: 9606.758 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P0A1L5
#2: Protein Flagellar biosynthetic protein FliR


Mass: 28938.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P54702
#3: Protein
Flagellar biosynthetic protein FliP


Mass: 26801.086 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P54700

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Protein , 4 types, 51 molecules KLMNOPQRSTUbcdefghijklZFZGZHZIZJZKZLZM...

#4: Protein
Flagellar hook-basal body complex protein FliE


Mass: 11087.662 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P26462
#5: Protein
Flagellar basal body rod protein FlgB / Putative proximal rod protein


Mass: 15145.061 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P16437
#7: Protein
Flagellar M-ring protein


Mass: 61295.645 Da / Num. of mol.: 11 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P15928
#10: Protein ...
Flagellar hook protein FlgE


Mass: 42233.152 Da / Num. of mol.: 29 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P0A1J1

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Flagellar basal-body rod protein ... , 3 types, 35 molecules VWXYZamnopq0123456789ZAZBZCZDZErstu...

#6: Protein
Flagellar basal-body rod protein FlgC / Putative proximal rod protein


Mass: 13991.889 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P0A1I7
#8: Protein
Flagellar basal-body rod protein FlgF / Putative proximal rod protein


Mass: 26121.223 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P16323
#9: Protein ...
Flagellar basal-body rod protein FlgG / Distal rod protein


Mass: 27784.807 Da / Num. of mol.: 24 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P0A1J3

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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 CW 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
111.7 mMtris(hydroxymethyl)aminomethane hydrochlorideTris-HCl1
24.17 mMethylenediaminetetraacetic acidEDTA1
30.083 %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

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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: 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

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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
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: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24190 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingDetails: Model-Angelo / Source name: Other / Type: in silico model

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