8Z5U | pdb_00008z5u

Cryo-EM structure of the rod-export apparatus with partial hook within the polar flagellar motor

• PDB DOI: https://doi.org/10.2210/pdb8Z5U/pdb
• EM Map EMD-39782: 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: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Cryo-EM structure of the rod-export apparatus with partial hook within 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 89-mer - A27B12C7D6E5F5G5H5I5J4K3L2M1N1O1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 89-mer - A44B6C5D5E5F5G4H2I2J1K1L1M1N1O1P1Q1R1S1T1 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 27-mer - A27 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 12-mer - B12 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - J4 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Hetero 15-mer - E5G5I5 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Hetero 12-mer - E4G2H2I2J2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 2,955.35 kDa 
• Atom Count: 118,072 
• Modeled Residue Count: 15,597 
• Deposited Residue Count: 27,193 
• Unique protein chains: 12

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar hook protein FlgE	A [auth D], B [auth E], C [auth F], D [auth G], E [auth H], F [auth I], G [auth J], H [auth K], I [auth L], J [auth M], K [auth N], L [auth O]	437	Vibrio alginolyticus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat protein	M [auth 0], V [auth 9]	199	Vibrio alginolyticus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar biosynthetic protein FliP	JC [auth y], KC [auth z], N [auth 1], O [auth 2], P [auth 3]	289	Vibrio alginolyticus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar biosynthetic protein FliQ	Q [auth 4], R [auth 5], S [auth 6], T [auth 7]	89	Vibrio alginolyticus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar biosynthetic protein FliR	U [auth 8]	260	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for A0A0H0YFV7 (Vibrio alginolyticus) Explore A0A0H0YFV7  Go to UniProtKB:  A0A0H0YFV7

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar basal-body rod protein FlgG	AB [auth P], BB [auth Q], CB [auth R], DB [auth S], EB [auth T], FB [auth U], GB [auth V], HB [auth W], IB [auth X], JB [auth Y], KB [auth Z], LB [auth a], MA [auth B], NA [auth C], OA [auth AP], PA [auth AQ], QA [auth AR], RA [auth AS], SA [auth AT], TA [auth AU], UA [auth AV], VA [auth AW], W [auth A], WA [auth AX], XA [auth AY], YA [auth AZ], ZA [auth Aa]	262	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for A0A0H0YB44 (Vibrio alginolyticus) Explore A0A0H0YB44  Go to UniProtKB:  A0A0H0YB44

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar M-ring protein	AA [auth AD], BA [auth AE], CA [auth AF], DA [auth AG], EA [auth AH], FA [auth AI], GA [auth AJ], HA [auth AK], IA [auth AL], JA [auth AM], KA [auth AN], LA [auth AO], X [auth AA], Y [auth AB], Z [auth AC]	580	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for Q75N27 (Vibrio alginolyticus) Explore Q75N27  Go to UniProtKB:  Q75N27

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar basal body rod protein FlgB	MB [auth b], NB [auth c], OB [auth d], PB [auth e], QB [auth f]	131	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for A0A0G9LZG6 (Vibrio alginolyticus) Explore A0A0G9LZG6  Go to UniProtKB:  A0A0G9LZG6

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar basal-body rod protein FlgC	RB [auth g], SB [auth h], TB [auth i], UB [auth j], VB [auth k], WB [auth l]	137	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for A0A0G9LZH2 (Vibrio alginolyticus) Explore A0A0G9LZH2  Go to UniProtKB:  A0A0G9LZH2

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar basal-body rod protein FlgF	AC [auth p], BC [auth q], XB [auth m], YB [auth n], ZB [auth o]	249	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for A0A0G9M4M9 (Vibrio alginolyticus) Explore A0A0G9M4M9  Go to UniProtKB:  A0A0G9M4M9

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar hook-basal body complex protein FliE	CC [auth r], DC [auth s], EC [auth t], FC [auth u], GC [auth v], HC [auth w]	103	Vibrio alginolyticus	Mutation(s): 0

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar biosynthetic protein FlhB	IC [auth x]	376	Vibrio alginolyticus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

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

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