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- PDB-7clr: CryoEM structure of S.typhimurium flagellar LP ring -

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Basic information

Entry
Database: PDB / ID: 7clr
TitleCryoEM structure of S.typhimurium flagellar LP ring
Components
  • Flagellar L-ring protein
  • Flagellar P-ring protein
KeywordsMOTOR PROTEIN / FlgH / FlgI / LP ring / Bushing / Salmonella / Flagellar motor
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
Similarity search - Domain/homology
Flagellar P-ring protein / Flagellar L-ring protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYamaguchi, T. / Makino, F. / Miyata, T. / Minamino, T. / Kato, T. / Namba, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP25000013,JP18K06155,JP26293097,JP19H03182,JP15H01640 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101117,JP17pc0101020 Japan
CitationJournal: Nat Commun / Year: 2021
Title: Structure of the molecular bushing of the bacterial flagellar motor.
Authors: Tomoko Yamaguchi / Fumiaki Makino / Tomoko Miyata / Tohru Minamino / Takayuki Kato / Keiichi Namba /
Abstract: The basal body of the bacterial flagellum is a rotary motor that consists of several rings (C, MS and LP) and a rod. The LP ring acts as a bushing supporting the distal rod for its rapid and stable ...The basal body of the bacterial flagellum is a rotary motor that consists of several rings (C, MS and LP) and a rod. The LP ring acts as a bushing supporting the distal rod for its rapid and stable rotation without much friction. Here, we use electron cryomicroscopy to describe the LP ring structure around the rod, at 3.5 Å resolution, from Salmonella Typhimurium. The structure shows 26-fold rotational symmetry and intricate intersubunit interactions of each subunit with up to six partners, which explains the structural stability. The inner surface is charged both positively and negatively. Positive charges on the P ring (the part of the LP ring that is embedded within the peptidoglycan layer) presumably play important roles in its initial assembly around the rod with a negatively charged surface.
History
DepositionJul 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: pdbx_database_related
Revision 1.2Dec 22, 2021Group: Database references / Category: citation / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)1,635,94252
Polymers1,635,94252
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: 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 / Details: SJW2177 / Source: (natural) Salmonella typhimurium (bacteria) / References: UniProt: A0A0F7J5J5
#2: 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 / Details: SJW2177 / Source: (natural) Salmonella typhimurium (bacteria) / References: UniProt: A0A0J5DWE9

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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: LP ring / Type: COMPLEX / Details: Bushing of flagellar motor / Entity ID: all / Source: NATURAL
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: HK1002
Source (recombinant)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris-HClTrisC4H11NO31
250 mMSodium chlorideNaClSodium chloride1
325 mMImidazoleC3H4N21
40.05 % (w/v)Lauryl Maltose Neopentyl Glycol(LMNG)C47H88O221
50.05 % (w/v)Triton X-1001
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: MOLYBDENUM / Grid type: Quantifoil R1.2/1.3
EM embeddingMaterial: buffer
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 200
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 40000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 275 nm / Calibrated defocus max: 8230 nm / Cs: 1.4 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingAverage exposure time: 10 sec. / Electron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 12759
EM imaging opticsEnergyfilter name: In-column Omega Filter
Image scansMovie frames/image: 50 / Used frames/image: 1-50

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Processing

EM software
IDNameVersionCategoryDetails
2RELION3image acquisitionbeta-2
4Gctf1.06CTF correction
7PHENIX1.13model fitting
8Coot0.8.9.1model fitting
9UCSF Chimera1.11.2model fitting
11PHENIX1.13model refinement
12Coot0.8.9.1model refinement
13RELION3.0 beta-2initial Euler assignment
14RELION3.0 beta-2final Euler assignment
15RELION3.0 beta-2classification
16RELION3.0 beta-23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 64418
Details: particles were picked up by YOLOPick.py (in-house python program)
SymmetryPoint symmetry: C26 (26 fold cyclic)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10802 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingB value: 38 / Protocol: OTHER / Space: REAL

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