9YDO | pdb_00009ydo

LPHT-ring in Vibrio cholerae at assembled, opened state

• PDB DOI: https://doi.org/10.2210/pdb9YDO/pdb
• EM Map EMD-72815: EMDB EMDataResource

• Classification: MOTOR PROTEIN
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Mutation(s): No 


• Deposited: 2025-09-22 Released: 2026-06-10 
• Deposition Author(s): Guo, W., Yue, J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.69 Å
• Aggregation State: CELL 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Near-atomic in situ architecture and membrane-coupled dynamics of the Vibrio cholerae sheathed flagellum.

Guo, W., Yue, J., Park, J.H., Valverde-Mendez, D., Botting, J.M., Yu, H., Sen, A., Kumar, R., Yan, J., Yildiz, F.H., Liu, J.

(2026) Nat Commun 17

• PubMed: 42660870 
• DOI: https://doi.org/10.1038/s41467-026-75593-6
• Primary Citation Related Structures: 
  9YDO


• PubMed Abstract: 
  

  The sheathed flagellum of Vibrio cholerae is a self-assembling membranous organelle that coordinates flagellar assembly, sheath biogenesis, and rapid rotation. Here, we determine in-situ near-atomic structures of the sheathed flagellar motor within intact cells. The motor anchors to the outer membrane through lipidated HL-rings without forming a membrane pore, thereby enabling flagellar assembly to drive sheath formation. Conserved LP-rings function as slide-rotary bushings, permitting high-speed rotation within the bacterial envelope while retaining the ability to constrict and seal the lumen upon flagellar ejection. We further show that stator activation depends on a specific protein-protein interaction rather than peptidoglycan engagement. Together, these findings reveal how the distinctive architecture and dynamics of the sheathed flagellum support V. cholerae motility, environmental survival, and persistent colonization of the human gut.

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Organizational Affiliation: 
• Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA.
Microbial Sciences Institute, Yale University, West Haven, CT, USA.
Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA. [e-mail].
Microbial Sciences Institute, Yale University, West Haven, CT, USA. [e-mail].
Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, USA.
Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, USA.
Quantitative Biology Institute, Yale University, New Haven, CT, USA.
Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, USA. [e-mail].
Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA. [e-mail].
Microbial Sciences Institute, Yale University, West Haven, CT, USA. [e-mail].
Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA. [e-mail].
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C26  (Explore in 3D)
Global Stoichiometry: Hetero 156-mer - A52B26C26D26E26 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 156-mer - AA26AB26AC26AD26AE1AF1AG1AH1AI1AJ1AK1AL1AM1AN1AO1AP1AQ1AR1AS1AT1AU1AV1AW1AX1AY1AZ1Aa1Ab1Ac1Ad1Ae1Af1Ag1Ah1Ai1Aj1Ak1Al1Am1An1Ao1Ap1Aq1Ar1As1At1Au1Av1Aw1Ax1Ay1Az1BA1BB1BC1BD1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3,501.12 kDa 
• Atom Count: 236,015 
• Modeled Residue Count: 30,589 
• Deposited Residue Count: 31,824 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar L-ring protein	A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As], T [auth At], U [auth Au], V [auth Av], W [auth Aw], X [auth Ax], Y [auth Ay], Z [auth Az]	227	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0
UniProt
Find proteins for Q9KQ13 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQ13  Go to UniProtKB:  Q9KQ13

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar P-ring protein	AA [auth Ba], BA [auth Bb], CA [auth Bc], DA [auth Bd], EA [auth Be], FA [auth Bf], GA [auth Bg], HA [auth Bh], IA [auth Bi], JA [auth Bj], KA [auth Bk], LA [auth Bl], MA [auth Bm], NA [auth Bn], OA [auth Bo], PA [auth Bp], QA [auth Bq], RA [auth Br], SA [auth Bs], TA [auth Bt], UA [auth Bu], VA [auth Bv], WA [auth Bw], XA [auth Bx], YA [auth By], ZA [auth Bz]	343	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0
UniProt
Find proteins for Q9KQ14 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQ14  Go to UniProtKB:  Q9KQ14

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar protein FlgT	AB [auth Ca], BB [auth Cb], CB [auth Cc], DB [auth Cd], EB [auth Ce], FB [auth Cf], GB [auth Cg], HB [auth Ch], IB [auth Ci], JB [auth Cj], KB [auth Ck], LB [auth Cl], MB [auth Cm], NB [auth Cn], OB [auth Co], PB [auth Cp], QB [auth Cq], RB [auth Cr], SB [auth Cs], TB [auth Ct], UB [auth Cu], VB [auth Cv], WB [auth Cw], XB [auth Cx], YB [auth Cy], ZB [auth Cz]	352	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0
UniProt
Find proteins for Q9KPZ9 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KPZ9  Go to UniProtKB:  Q9KPZ9

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium-type flagellar protein MotY	AC [auth Da], BC [auth Db], CC [auth Dc], DC [auth Dd], EC [auth De], FC [auth Df], GC [auth Dg], HC [auth Dh], IC [auth Di], JC [auth Dj], KC [auth Dk], LC [auth Dl], MC [auth Dm], NC [auth Dn], OC [auth Do], PC [auth Dp], QC [auth Dq], RC [auth Dr], SC [auth Ds], TC [auth Dt], UC [auth Du], VC [auth Dv], WC [auth Dw], XC [auth Dx], YC [auth Dy], ZC [auth Dz]	272	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0
UniProt
Find proteins for Q9KT95 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KT95  Go to UniProtKB:  Q9KT95

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar assembly lipoprotein FlgP	AD [auth Fa], AE [auth Ga], BD [auth Fb], BE [auth Gb], CD [auth Fc], CE [auth Gc], DD [auth Fd], DE [auth Gd], ED [auth Fe], EE [auth Ge], FD [auth Ff], FE [auth Gf], GD [auth Fg], GE [auth Gg], HD [auth Fh], HE [auth Gh], ID [auth Fi], IE [auth Gi], JD [auth Fj], JE [auth Gj], KD [auth Fk], KE [auth Gk], LD [auth Fl], LE [auth Gl], MD [auth Fm], ME [auth Gm], ND [auth Fn], NE [auth Gn], OD [auth Fo], OE [auth Go], PD [auth Fp], PE [auth Gp], QD [auth Fq], QE [auth Gq], RD [auth Fr], RE [auth Gr], SD [auth Fs], SE [auth Gs], TD [auth Ft], TE [auth Gt], UD [auth Fu], UE [auth Gu], VD [auth Fv], VE [auth Gv], WD [auth Fw], WE [auth Gw], XD [auth Fx], XE [auth Gx], YD [auth Fy], YE [auth Gy], ZD [auth Fz], ZE [auth Gz]	15	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0
UniProt
Find proteins for A0A2V4N6M7 (Vibrio cholerae) Explore A0A2V4N6M7  Go to UniProtKB:  A0A2V4N6M7

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.69 Å
• Aggregation State: CELL 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-10 
Deposition Author(s): Guo, W., Yue, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI087946
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI132818

Revision History  

• Version 1.0: 2026-06-10
  Type: Initial release
  
• Version 1.1: 2026-10-21
  Changes: Data collection, Database references