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- PDB-8z5w: Cryo-EM structure of the LRR protein within the polar flagellar motor -

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Basic information

Entry
Database: PDB / ID: 8z5w
TitleCryo-EM structure of the LRR protein within the polar flagellar motor
Components
  • (Flagellar basal-body rod protein ...) x 3
  • Flagellar M-ring protein
  • Flagellar basal body rod protein FlgB
  • Leucine-rich repeat protein
KeywordsMOTOR PROTEIN / Polar flagellum / Polar flagellar motor / LRR
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum-dependent swarming motility / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / plasma membrane
Similarity search - Function
Flagellar basal-body rod FlgF / Flagellar basal-body rod FlgG / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgB / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. ...Flagellar basal-body rod FlgF / Flagellar basal-body rod FlgG / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgB / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / 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 FlgB / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgF / Flagellar basal-body rod protein FlgG / : / Flagellar M-ring protein
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsZhang, L. / Tan, J.X. / 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: Protein Cell / Year: 2026
Title: Molecular basis of high-torque transmission of the Vibrio polar flagellar motor.
Authors: Ling Zhang / Jiaxing Tan / Xuemin Duan / Xiaofei Wang / Ting Wang / Keke Yuan / Michio Homma / Seiji Kojima / Yan Zhou / Yongqun Zhu /
Abstract: The bacterial flagellar motor is a protein nanomachine that rotates the flagellum to facilitate bacterial motility. These motors exhibit structural diversity among species, enabling the transmission ...The bacterial flagellar motor is a protein nanomachine that rotates the flagellum to facilitate bacterial motility. These motors exhibit structural diversity among species, enabling the transmission of varying torques to flagellar filaments to grant bacteria diverse swimming capabilities. Compared to peritrichous flagellar motors, polar flagellar motors are faster machines that transmit higher torque to drive high-speed motility in liquids and empower swimming in viscous environments. However, structural basis of high-torque transmission of the polar flagellar motors is still unclear. Here we present a cryo-electron microscopy structure of the polar flagellar motor in complex with the hook from Vibrio alginolyticus, comprising 295 subunits from 18 proteins. Compared to the peritrichous flagellar rod, this structure reveals an increased number of inter-subunit interactions in the rod of the polar flagellar motor. Nine phospholipid molecules insert into the interface between the export apparatus and the proximal rod. The LP ring contains more electrostatic charges on the inner surface and has fewer physical contacts with the rod, while the HT ring tightly binds to the outer surface of the LP ring. FlrP, a protein of previously unknown function, is identified as a new component of the polar flagellar motor, and extensively participates in the interactions of 15 FliF peptides of the MS ring with the rod. In contrast to that in the peritrichous flagellum, the hook in the polar flagellum has two different conformational states, L- and R-types. These findings provide unprecedented insights into structural adaptations of the bacterial polar flagellar motors for high-torque transmission.
History
DepositionApr 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Leucine-rich repeat protein
9: Leucine-rich repeat protein
A: Flagellar basal-body rod protein FlgG
AA: Flagellar M-ring protein
AB: Flagellar M-ring protein
AC: Flagellar M-ring protein
AD: Flagellar M-ring protein
AE: Flagellar M-ring protein
AF: Flagellar M-ring protein
AG: Flagellar M-ring protein
AH: Flagellar M-ring protein
AI: Flagellar M-ring protein
AJ: Flagellar M-ring protein
AK: Flagellar M-ring protein
AL: Flagellar M-ring protein
AM: Flagellar M-ring protein
AN: Flagellar M-ring protein
AO: Flagellar M-ring protein
B: Flagellar basal-body rod protein FlgG
C: Flagellar basal-body rod protein FlgG
AP: Flagellar basal-body rod protein FlgG
AQ: Flagellar basal-body rod protein FlgG
AR: Flagellar basal-body rod protein FlgG
b: Flagellar basal body rod protein FlgB
c: Flagellar basal body rod protein FlgB
d: Flagellar basal body rod protein FlgB
e: Flagellar basal body rod protein FlgB
f: Flagellar basal body rod protein FlgB
g: Flagellar basal-body rod protein FlgC
h: Flagellar basal-body rod protein FlgC
i: Flagellar basal-body rod protein FlgC
j: Flagellar basal-body rod protein FlgC
k: Flagellar basal-body rod protein FlgC
l: Flagellar basal-body rod protein FlgC
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


Theoretical massNumber of molelcules
Total (without water)1,464,23639
Polymers1,464,23639
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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Protein , 3 types, 22 molecules 09AAABACADAEAFAGAHAIAJAKALAMANAObcdef

#1: Protein Leucine-rich repeat protein


Mass: 21518.053 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A9W4FN72
#3: Protein
Flagellar M-ring protein


Mass: 63915.605 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: Q75N27
#4: Protein
Flagellar basal body rod protein FlgB


Mass: 14239.950 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A0G9LZG6

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Flagellar basal-body rod protein ... , 3 types, 17 molecules ABCAPAQARghijklmnopq

#2: Protein
Flagellar basal-body rod protein FlgG / Distal rod protein


Mass: 27908.943 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A0H0YB44
#5: Protein
Flagellar basal-body rod protein FlgC


Mass: 14812.569 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A0G9LZH2
#6: Protein
Flagellar basal-body rod protein FlgF


Mass: 26987.387 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A0G9M4M9

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Details

Has protein modificationN

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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: The polar flagellar motor-hook complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Buffer solutionpH: 8
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: 277.15 K

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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
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
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7Cootmodel fitting
8UCSF ChimeraXmodel fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
14PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 329955
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19450 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: in silico model

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