8Z5S | pdb_00008z5s

Cryo-EM structure of the proximal rod-export apparatus of the polar flagellar motor

• PDB DOI: https://doi.org/10.2210/pdb8Z5S/pdb
• EM Map EMD-39780: 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)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Cryo-EM structure of the proximal rod-export apparatus of the polar flagellar motor

Zhang, L., Tan, J.X., Zhou, Y., Zhu, Y.Q.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 48-mer - A7B6C5D5E5F5G5H4I3J1K1L1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 48-mer - A6B5C5D5E5F5G4H2I1J1K1L1M1N1O1P1Q1R1S1 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - H4 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Hetero 15-mer - C5E5G5 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Hetero 10-mer - C4E2G2H2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,589.56 kDa 
• Atom Count: 38,336 
• Modeled Residue Count: 5,016 
• Deposited Residue Count: 14,477 
• Unique protein chains: 9

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar biosynthetic protein FliP	A [auth 1], B [auth 2], C [auth 3], UA [auth y], VA [auth z]	289	Vibrio alginolyticus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar biosynthetic protein FliQ	D [auth 4], E [auth 5], F [auth 6], G [auth 7]	89	Vibrio alginolyticus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar biosynthetic protein FliR	H [auth 8]	260	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for A0A0H0YFV7 (Vibrio alginolyticus) Explore A0A0H0YFV7  Go to UniProtKB:  A0A0H0YFV7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar M-ring protein	I [auth AA], J [auth AB], K [auth AC], L [auth AD], M [auth AE], N [auth AF], O [auth AG], P [auth AH], Q [auth AI], R [auth AJ], S [auth AK], T [auth AL], U [auth AM], V [auth AN], W [auth AO]	580	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for Q75N27 (Vibrio alginolyticus) Explore Q75N27  Go to UniProtKB:  Q75N27

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar basal body rod protein FlgB	AA [auth e], BA [auth f], X [auth b], Y [auth c], Z [auth d]	131	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for A0A0G9LZG6 (Vibrio alginolyticus) Explore A0A0G9LZG6  Go to UniProtKB:  A0A0G9LZG6

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar basal-body rod protein FlgC	CA [auth g], DA [auth h], EA [auth i], FA [auth j], GA [auth k], HA [auth l]	137	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for A0A0G9LZH2 (Vibrio alginolyticus) Explore A0A0G9LZH2  Go to UniProtKB:  A0A0G9LZH2

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar basal-body rod protein FlgF	IA [auth m], JA [auth n], KA [auth o], LA [auth p], MA [auth q]	249	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for A0A0G9M4M9 (Vibrio alginolyticus) Explore A0A0G9M4M9  Go to UniProtKB:  A0A0G9M4M9

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar hook-basal body complex protein FliE	NA [auth r], OA [auth s], PA [auth t], QA [auth u], RA [auth v], SA [auth w]	103	Vibrio alginolyticus	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar biosynthetic protein FlhB	TA [auth x]	376	Vibrio alginolyticus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.03 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.

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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