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- PDB-8wle: Cryo-EM structure of the LP ring within the flagellar motor-hook ... -

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Basic information

Entry
Database: PDB / ID: 8wle
TitleCryo-EM structure of the LP ring within the flagellar motor-hook complex in the CCW state.
Components
  • Flagellar L-ring protein
  • Flagellar P-ring protein
KeywordsMOTOR PROTEIN / Flagellum / Flagellar motor / LP ring
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum basal body, distal rod, P ring / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / cell outer membrane / outer membrane-bounded periplasmic space / structural molecule activity
Similarity search - Function
Flagellar L-ring protein / Flagellar L-ring protein / Flagellar P-ring protein / Flagellar P-ring protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Flagellar L-ring protein / Flagellar P-ring protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 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 LP ring within the flagellar motor-hook complex in the CCW state.
Authors: Tan, J.X. / Zhang, L. / Zhou, Y. / Zhu, Y.Q.
History
DepositionSep 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellar L-ring protein
a: Flagellar P-ring protein
B: Flagellar L-ring protein
b: Flagellar P-ring protein
C: Flagellar L-ring protein
c: Flagellar P-ring protein
D: Flagellar L-ring protein
d: Flagellar P-ring protein
E: Flagellar L-ring protein
e: Flagellar P-ring protein
F: Flagellar L-ring protein
f: Flagellar P-ring protein
G: Flagellar L-ring protein
g: Flagellar P-ring protein
H: Flagellar L-ring protein
h: Flagellar P-ring protein
I: Flagellar L-ring protein
i: Flagellar P-ring protein
J: Flagellar L-ring protein
j: Flagellar P-ring protein
K: Flagellar L-ring protein
k: Flagellar P-ring protein
L: Flagellar L-ring protein
l: Flagellar P-ring protein
M: Flagellar L-ring protein
m: Flagellar P-ring protein
N: Flagellar L-ring protein
n: Flagellar P-ring protein
O: Flagellar L-ring protein
o: Flagellar P-ring protein
P: Flagellar L-ring protein
p: Flagellar P-ring protein
Q: Flagellar L-ring protein
q: Flagellar P-ring protein
R: Flagellar L-ring protein
r: Flagellar P-ring protein
S: Flagellar L-ring protein
s: Flagellar P-ring protein
T: Flagellar L-ring protein
t: Flagellar P-ring protein
U: Flagellar L-ring protein
u: Flagellar P-ring protein
V: Flagellar L-ring protein
v: Flagellar P-ring protein
W: Flagellar L-ring protein
w: Flagellar P-ring protein
X: Flagellar L-ring protein
x: Flagellar P-ring protein
Y: Flagellar L-ring protein
y: Flagellar P-ring protein
Z: Flagellar L-ring protein
z: Flagellar P-ring protein


Theoretical massNumber of molelcules
Total (without water)1,635,94252
Polymers1,635,94252
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 L-ring protein / Basal body L-ring protein


Mass: 24726.666 Da / Num. of mol.: 26 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P0A1N8
#2: Protein ...
Flagellar P-ring protein / Basal body P-ring protein


Mass: 38194.176 Da / Num. of mol.: 26 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P15930
Has protein modificationY

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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 %octylphenol ethoxylateTX-1001
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: Blot time: 2 Blot force: -15 Wait time: 60 Blot total: 1

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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: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 45 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1.1particle selection
2SerialEMimage 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: 22192 / Details: Particles were manually picked using cryoSPARC
SymmetryPoint symmetry: C26 (26 fold cyclic)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11858 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 7CBL

7cbl


Accession code: 7CBL / Source name: PDB / Type: experimental model

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