8Z5N | pdb_00008z5n

Cryo-EM structure of the LPHT ring

• PDB DOI: https://doi.org/10.2210/pdb8Z5N/pdb
• EM Map EMD-39776: 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: 2.95 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Cryo-EM structure of the LPHT ring

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C26  (Explore in 3D)
Global Stoichiometry: Hetero 182-mer - A26B26C26D26E26F26G26 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 182-mer - AA26AB26AC26AD26AE26AF1AG1AH1AI1AJ1AK1AL1AM1AN1AO1AP1AQ1AR1AS1AT1AU1AV1AW1AX1AY1AZ1Aa1Ab1Ac1Ad1Ae1Af1Ag1Ah1Ai1Aj1Ak1Al1Am1An1Ao1Ap1Aq1Ar1As1At1Au1Av1Aw1Ax1Ay1Az1BA1BB1BC1BD1BE1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 4,773.87 kDa 
• Atom Count: 269,711 
• Modeled Residue Count: 34,671 
• Deposited Residue Count: 43,134 
• Unique protein chains: 7

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Component of sodium-driven polar flagellar motor	A, B, CA [auth c], DA [auth d], E, F, GA [auth g], HA [auth h], I, J, KA [auth k], LA [auth l], M, N, OA [auth o], PA [auth p], Q, R, SA [auth s], TA [auth t], U, V, WA [auth w], XA [auth x], Y, Z	293	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for P74944 (Vibrio alginolyticus) Explore P74944  Go to UniProtKB:  P74944

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium-type flagellar motor component	AA [auth a], BA [auth b], C, D, EA [auth e], FA [auth f], G, H, IA [auth i], JA [auth j], K, L, MA [auth m], NA [auth n], O, P, QA [auth q], RA [auth r], S, T, UA [auth u], VA [auth v], W, X, YA [auth y], ZA [auth z]	211	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for Q93R25 (Vibrio alginolyticus) Explore Q93R25  Go to UniProtKB:  Q93R25

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar L-ring protein	AB [auth 1], BF [auth Bh], CE [auth BI], DD [auth At], EC [auth AU], FB [auth 6], GF [auth Bm], HE [auth BN], ID [auth Ay], JC [auth AZ], KB [auth AA], LF [auth Br], ME [auth BS], ND [auth A4], OC [auth Ae], PB [auth AF], QF [auth Bw], RE [auth BX], SD [auth A9], TC [auth Aj], UB [auth AK], VF [auth B2], WE [auth Bc], XD [auth BD], YC [auth Ao], ZB [auth AP]	259	Vibrio alginolyticus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar assembly lipoprotein FlgP	AC [auth AQ], BB [auth 2], CF [auth Bi], DE [auth BJ], ED [auth Au], FC [auth AV], GB [auth 7], HF [auth Bn], IE [auth BO], JD [auth Az], KC [auth Aa], LB [auth AB], MF [auth Bs], NE [auth BT], OD [auth A5], PC [auth Af], QB [auth AG], RF [auth Bx], SE [auth BY], TD [auth A0], UC [auth Ak], VB [auth AL], WF [auth B3], XE [auth Bd], YD [auth BE], ZC [auth Ap]	143	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for A0A0H0Y943 (Vibrio alginolyticus) Explore A0A0H0Y943  Go to UniProtKB:  A0A0H0Y943

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
The N-terminus of Flagellar L-ring protein	AD [auth Aq], BC [auth AR], CB [auth 3], DF [auth Bj], EE [auth BK], FD [auth Av], GC [auth AW], HB [auth 8], IF [auth Bo], JE [auth BP], KD [auth A1], LC [auth Ab], MB [auth AC], NF [auth Bt], OE [auth BU], PD [auth A6], QC [auth Ag], RB [auth AH], SF [auth By], TE [auth BZ], UD [auth BA], VC [auth Al], WB [auth AM], XF [auth B4], YE [auth Be], ZD [auth BF]	13	Vibrio alginolyticus	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar P-ring protein	AE [auth BG], BD [auth Ar], CC [auth AS], DB [auth 4], EF [auth Bk], FE [auth BL], GD [auth Aw], HC [auth AX], IB [auth 9], JF [auth Bp], KE [auth BQ], LD [auth A2], MC [auth Ac], NB [auth AD], OF [auth Bu], PE [auth BV], QD [auth A7], RC [auth Ah], SB [auth AI], TF [auth Bz], UE [auth Ba], VD [auth BB], WC [auth Am], XB [auth AN], YF [auth B5], ZE [auth Bf]	363	Vibrio alginolyticus	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagella basal-body protein	AF [auth Bg], BE [auth BH], CD [auth As], DC [auth AT], EB [auth 5], FF [auth Bl], GE [auth BM], HD [auth Ax], IC [auth AY], JB [auth 0], KF [auth Bq], LE [auth BR], MD [auth A3], NC [auth Ad], OB [auth AE], PF [auth Bv], QE [auth BW], RD [auth A8], SC [auth Ai], TB [auth AJ], UF [auth B1], VE [auth Bb], WD [auth BC], XC [auth An], YB [auth AO], ZF [auth B6]	377	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for D9N551 (Vibrio alginolyticus) Explore D9N551  Go to UniProtKB:  D9N551

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.95 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