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- PDB-7cbl: Cryo-EM structure of the flagellar LP ring from Salmonella -

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Basic information

Entry
Database: PDB / ID: 7cbl
TitleCryo-EM structure of the flagellar LP ring from Salmonella
Components
  • Flagellar L-ring protein
  • Flagellar P-ring protein
KeywordsMOTOR PROTEIN / Flagella / LP ring / FlgH / FlgI
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
OCTANOIC ACID (CAPRYLIC ACID) / Flagellar L-ring protein / Flagellar P-ring protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsTan, J.X. / Chang, S.H. / Wang, X.F. / Xu, C.H. / Zhou, Y. / Zhang, X. / Zhu, Y.Q.
Funding support China, 6items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0504803 China
Ministry of Science and Technology (MoST, China)2018YFA0507700 China
Ministry of Science and Technology (MoST, China)2017YFA0503900 China
National Natural Science Foundation of China (NSFC)81925024 China
National Natural Science Foundation of China (NSFC)81530068 China
National Natural Science Foundation of China (NSFC)81501717 China
CitationJournal: Cell / Year: 2021
Title: Structural basis of assembly and torque transmission of the bacterial flagellar motor.
Authors: Jiaxing Tan / Xing Zhang / Xiaofei Wang / Caihuang Xu / Shenghai Chang / Hangjun Wu / Ting Wang / Huihui Liang / Haichun Gao / Yan Zhou / Yongqun Zhu /
Abstract: The bacterial flagellar motor is a supramolecular protein machine that drives rotation of the flagellum for motility, which is essential for bacterial survival in different environments and a key ...The bacterial flagellar motor is a supramolecular protein machine that drives rotation of the flagellum for motility, which is essential for bacterial survival in different environments and a key determinant of pathogenicity. The detailed structure of the flagellar motor remains unknown. Here we present an atomic-resolution cryoelectron microscopy (cryo-EM) structure of the bacterial flagellar motor complexed with the hook, consisting of 175 subunits with a molecular mass of approximately 6.3 MDa. The structure reveals that 10 peptides protruding from the MS ring with the FlgB and FliE subunits mediate torque transmission from the MS ring to the rod and overcome the symmetry mismatch between the rotational and helical structures in the motor. The LP ring contacts the distal rod and applies electrostatic forces to support its rotation and torque transmission to the hook. This work provides detailed molecular insights into the structure, assembly, and torque transmission mechanisms of the flagellar motor.
History
DepositionJun 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 26, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,639,69178
Polymers1,635,94252
Non-polymers3,74926
Water00
1


  • Idetical with deposited unit
  • defined by author
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 typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (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 typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P15930
#3: Chemical...
ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C8H16O2
Has ligand of interestN

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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: Flagellar hook-basal body / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMtris(hydroxymethyl)aminomethane hydrochloride-hydrochlorideTris-HCl1
25 mMethylene diamine tetraacetic 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: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K / Details: blot for 6 seconds before plunging

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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: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 47 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C26 (26 fold cyclic)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80548 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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