8Z5Y | pdb_00008z5y

Cryo-EM structure of the L-hook of the polar flagellum

• PDB DOI: https://doi.org/10.2210/pdb8Z5Y/pdb
• EM Map EMD-39788: EMDB EMDataResource

• Classification: MOTOR PROTEIN
• Organism(s): Vibrio alginolyticus
• Mutation(s): No 


• Deposited: 2024-04-18 Released: 2025-10-22 
• Deposition Author(s): Zhang, L., Tan, J.X., Zhou, Y., Zhu, Y.Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Molecular basis of high-torque transmission of the Vibrio polar flagellar motor.

Zhang, L., Tan, J., Duan, X., Wang, X., Wang, T., Yuan, K., Homma, M., Kojima, S., Zhou, Y., Zhu, Y.

(2026) Protein Cell 

• PubMed: 41871453 
• DOI: https://doi.org/10.1093/procel/pwag025
• Primary Citation Related Structures: 
  8Z5N, 8Z5S, 8Z5U, 8Z5V, 8Z5W, 8Z5X, 8Z5Y, 8Z5Z, 8Z60


• PubMed 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 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.

---

Organizational Affiliation: 
• School of Public Health, Life Sciences Institute, and Department of Infectious Diseases of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China.
The MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.
State Key Laboratory for Vegetation Structure, Function and Construction, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China.
Department of Physics, Nagoya University, Nagoya, 464-8601, Japan.
Department of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8601, Japan.
Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, 310058, China.
Cancer Center, Zhejiang University, Hangzhou, 310058, China.
New Cornerstone Science Laboratory, Shenzhen, 518054, China.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 40-mer - A40 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,897.38 kDa 
• Atom Count: 132,760 
• Modeled Residue Count: 17,400 
• Deposited Residue Count: 17,480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar hook protein FlgE	A [auth D], AA [auth d], B [auth E], BA [auth e], C [auth F], CA [auth f], D [auth G], DA [auth g], E [auth H], EA [auth h], F [auth I], FA [auth i], G [auth J], GA [auth j], H [auth K], HA [auth k], I [auth L], IA [auth l], J [auth M], JA [auth m], K [auth N], KA [auth n], L [auth O], LA [auth o], M [auth P], MA [auth p], N [auth Q], NA [auth q], O [auth R], P [auth S], Q [auth T], R [auth U], S [auth V], T [auth W], U [auth X], V [auth Y], W [auth Z], X [auth a], Y [auth b], Z [auth c]	437	Vibrio alginolyticus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Zhang, L., Tan, J.X., Zhou, Y., Zhu, Y.Q.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81925024
National Natural Science Foundation of China (NSFC)	China	U23A20163
Ministry of Science and Technology (MoST, China)	China	2017YFA0503900

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release
  
• Version 1.1: 2026-05-13
  Changes: Data collection, Database references