9YH6 | pdb_00009yh6

Composite structure of the sheathed flagellar motor in Vibrio cholerae adopting a lower FOMC conformation

PDB DOI: https://doi.org/10.2210/pdb9YH6/pdb
EM Map EMD-72961: EMDB EMDataResource

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

Deposited: 2025-09-30 Released: 2026-06-10
Deposition Author(s): Guo, W.B., Yue, J., Liu, J.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: CELL
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

In-situ cryo-EM structures reveal mechanisms of sheathed flagellar assembly, rotation, and disassembly in Vibrio cholerae

Wangbiao, G., Jian, Y., Rajeev, K., Jun, L.

To be published.

Macromolecule Content

Total Structure Weight: 8,664.81 kDa
Atom Count: 574,924
Modeled Residue Count: 73,994
Deposited Residue Count: 78,133
Unique protein chains: 13

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar basal-body rod protein FlgG	A [auth Aa] B [auth Ab] BA [auth Bb] C [auth Ac] D [auth Ad] A [auth Aa], B [auth Ab], BA [auth Bb], 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]	262	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_2195
UniProt
Find proteins for Q9KQ12 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQ12 Go to UniProtKB: Q9KQ12
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KQ12
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar basal-body rod protein FlgF	AA [auth Ba], CA [auth Bc], DA [auth Bd], VA [auth Bv], WA [auth Bw]	249	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_2196
UniProt
Find proteins for Q9KQ11 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQ11 Go to UniProtKB: Q9KQ11
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KQ11
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar hook protein FlgE	EA [auth Be] FA [auth Bf] GA [auth Bg] HA [auth Bh] IA [auth Bi] 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]	434	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_2197
UniProt
Find proteins for Q9KQ10 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQ10 Go to UniProtKB: Q9KQ10
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KQ10
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar L-ring protein	AB [auth Ca] BB [auth Cb] CB [auth Cc] DB [auth Cd] EB [auth Ce] 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], XA [auth Bx], YA [auth By], ZA [auth Bz]	227	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: flgH, VC_2194
UniProt
Find proteins for Q9KQ13 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQ13 Go to UniProtKB: Q9KQ13
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KQ13
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar P-ring protein	AC [auth Da] BC [auth Db] CC [auth Dc] DC [auth Dd] EC [auth De] 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], XB [auth Cx], YB [auth Cy], ZB [auth Cz]	343	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: flgI, VC_2193
UniProt
Find proteins for Q9KQ14 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQ14 Go to UniProtKB: Q9KQ14
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KQ14
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar protein FlgT	AD [auth Ea] BD [auth Eb] CD [auth Ec] DD [auth Ed] ED [auth Ee] AD [auth Ea], BD [auth Eb], CD [auth Ec], DD [auth Ed], ED [auth Ee], FD [auth Ef], GD [auth Eg], HD [auth Eh], ID [auth Ei], JD [auth Ej], KD [auth Ek], LD [auth El], MD [auth Em], ND [auth En], OD [auth Eo], PD [auth Ep], QD [auth Eq], RD [auth Er], SD [auth Es], TD [auth Et], UD [auth Eu], VD [auth Ev], WD [auth Ew], XC [auth Dx], YC [auth Dy], ZC [auth Dz]	352	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_2208
UniProt
Find proteins for Q9KPZ9 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KPZ9 Go to UniProtKB: Q9KPZ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KPZ9
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium-type flagellar protein MotY	AE [auth Fa] BE [auth Fb] CE [auth Fc] DE [auth Fd] EE [auth Fe] AE [auth Fa], BE [auth Fb], CE [auth Fc], DE [auth Fd], EE [auth Fe], FE [auth Ff], GE [auth Fg], HE [auth Fh], IE [auth Fi], JE [auth Fj], KE [auth Fk], LE [auth Fl], ME [auth Fm], NE [auth Fn], OE [auth Fo], PE [auth Fp], QE [auth Fq], RE [auth Fr], SE [auth Fs], TE [auth Ft], UE [auth Fu], VE [auth Fv], WE [auth Fw], XD [auth Ex], YD [auth Ey], ZD [auth Ez]	271	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_1008
UniProt
Find proteins for Q9KT95 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KT95 Go to UniProtKB: Q9KT95
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KT95
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium-type flagellar protein MotX	AF [auth Ga] BF [auth Gb] CF [auth Gc] DF [auth Gd] EF [auth Ge] AF [auth Ga], BF [auth Gb], CF [auth Gc], DF [auth Gd], EF [auth Ge], FF [auth Gf], GF [auth Gg], HF [auth Gh], IF [auth Gi], JF [auth Gj], KF [auth Gk], LF [auth Gl], MF [auth Gm], NF [auth Gn], OF [auth Go], PF [auth Gp], QF [auth Gq], RF [auth Gr], SF [auth Gs], TF [auth Gt], UF [auth Gu], VF [auth Gv], WF [auth Gw], XE [auth Fx], YE [auth Fy], ZE [auth Fz]	183	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_2601
UniProt
Find proteins for Q9KNX9 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KNX9 Go to UniProtKB: Q9KNX9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KNX9
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Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
FlgP	AG [auth Ha] AH [auth Ia] BG [auth Hb] BH [auth Ib] CG [auth Hc] AG [auth Ha], AH [auth Ia], BG [auth Hb], BH [auth Ib], CG [auth Hc], CH [auth Ic], DG [auth Hd], DH [auth Id], EG [auth He], EH [auth Ie], FG [auth Hf], FH [auth If], GG [auth Hg], GH [auth Ig], HG [auth Hh], HH [auth Ih], IG [auth Hi], IH [auth Ii], JG [auth Hj], JH [auth Ij], KG [auth Hk], KH [auth Ik], LG [auth Hl], LH [auth Il], MG [auth Hm], MH [auth Im], NG [auth Hn], NH [auth In], OG [auth Ho], OH [auth Io], PG [auth Hp], PH [auth Ip], QG [auth Hq], QH [auth Iq], RG [auth Hr], RH [auth Ir], SG [auth Hs], SH [auth Is], TG [auth Ht], TH [auth It], UG [auth Hu], UH [auth Iu], VG [auth Hv], VH [auth Iv], WG [auth Hw], WH [auth Iw], XF [auth Gx], XG [auth Hx], YF [auth Gy], YG [auth Hy], ZF [auth Gz], ZG [auth Hz]	12	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Chemotaxis protein PomB	AI [auth Ja] BI [auth Jb] CI [auth Jc] DI [auth Jd] EI [auth Je] AI [auth Ja], BI [auth Jb], CI [auth Jc], DI [auth Jd], EI [auth Je], FI [auth Jf], GI [auth Jg], HI [auth Jh], II [auth Ji], JI [auth Jj], KI [auth Jk], LI [auth Jl], MI [auth Jm], NI [auth Jn], OI [auth Jo], PI [auth Jp], QI [auth Jq], RI [auth Jr], SI [auth Js], TI [auth Jt], UI [auth Ju], VI [auth Jv], WI [auth Jw], XH [auth Ix], YH [auth Iy], ZH [auth Iz]	155	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_0893
UniProt
Find proteins for Q9KTK9 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KTK9 Go to UniProtKB: Q9KTK9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KTK9
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Reference Sequence

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| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein	AJ [auth Ka] AK [auth La] AL [auth Ma] BJ [auth Kb] BK [auth Lb] AJ [auth Ka], AK [auth La], AL [auth Ma], BJ [auth Kb], BK [auth Lb], BL [auth Mb], CJ [auth Kc], CK [auth Lc], CL [auth Mc], DJ [auth Kd], DK [auth Ld], EJ [auth Ke], EK [auth Le], FJ [auth Kf], FK [auth Lf], GJ [auth Kg], GK [auth Lg], HJ [auth Kh], HK [auth Lh], IJ [auth Ki], IK [auth Li], JJ [auth Kj], JK [auth Lj], KJ [auth Kk], KK [auth Lk], LJ [auth Kl], LK [auth Ll], MJ [auth Km], MK [auth Lm], NJ [auth Kn], NK [auth Ln], OJ [auth Ko], OK [auth Lo], PJ [auth Kp], PK [auth Lp], QJ [auth Kq], QK [auth Lq], RJ [auth Kr], RK [auth Lr], SJ [auth Ks], SK [auth Ls], TJ [auth Kt], TK [auth Lt], UJ [auth Ku], UK [auth Lu], VJ [auth Kv], VK [auth Lv], WJ [auth Kw], WK [auth Lw], XI [auth Jx], XJ [auth Kx], XK [auth Lx], YI [auth Jy], YJ [auth Ky], YK [auth Ly], ZI [auth Jz], ZJ [auth Kz], ZK [auth Lz]	105	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_2206
UniProt
Find proteins for Q9KQ01 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQ01 Go to UniProtKB: Q9KQ01
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KQ01
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Reference Sequence

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| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
FlgO domain-containing protein	AM [auth Na] AN [auth Oa] BM [auth Nb] BN [auth Ob] CM [auth Nc] AM [auth Na], AN [auth Oa], BM [auth Nb], BN [auth Ob], CM [auth Nc], CN [auth Oc], DL [auth Md], DM [auth Nd], DN [auth Od], EL [auth Me], EM [auth Ne], EN [auth Oe], FL [auth Mf], FM [auth Nf], FN [auth Of], GL [auth Mg], GM [auth Ng], GN [auth Og], HL [auth Mh], HM [auth Nh], HN [auth Oh], IL [auth Mi], IM [auth Ni], IN [auth Oi], JL [auth Mj], JM [auth Nj], KL [auth Mk], KM [auth Nk], LL [auth Ml], LM [auth Nl], ML [auth Mm], MM [auth Nm], NL [auth Mn], NM [auth Nn], OL [auth Mo], OM [auth No], PL [auth Mp], PM [auth Np], QL [auth Mq], QM [auth Nq], RL [auth Mr], RM [auth Nr], SL [auth Ms], SM [auth Ns], TL [auth Mt], TM [auth Nt], UL [auth Mu], UM [auth Nu], VL [auth Mv], VM [auth Nv], WL [auth Mw], WM [auth Nw], XL [auth Mx], XM [auth Nx], YL [auth My], YM [auth Ny], ZL [auth Mz], ZM [auth Nz]	190	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_2207
UniProt
Find proteins for Q9KQ00 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQ00 Go to UniProtKB: Q9KQ00
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KQ00
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Reference Sequence

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| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
FliF	AO [auth Pa] BO [auth Pb] CO [auth Pc] DO [auth Pd] EO [auth Pe] AO [auth Pa], BO [auth Pb], CO [auth Pc], DO [auth Pd], EO [auth Pe], FO [auth Pf], GO [auth Pg], HO [auth Ph], IO [auth Pi], JN [auth Oj], JO [auth Pj], KN [auth Ok], KO [auth Pk], LN [auth Ol], LO [auth Pl], MN [auth Om], MO [auth Pm], NN [auth On], NO [auth Pn], ON [auth Oo], OO [auth Po], PN [auth Op], PO [auth Pp], QN [auth Oq], QO [auth Pq], RN [auth Or], SN [auth Os], TN [auth Ot], UN [auth Ou], VN [auth Ov], WN [auth Ow], XN [auth Ox], YN [auth Oy], ZN [auth Oz]	144	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-10

Deposition Author(s):

Guo, W.B.

Yue, J.

Liu, J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI189907
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI087946
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI132818
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI189907
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R37AI102584

Revision History (Full details and data files)

Version 1.0: 2026-06-10
Type: Initial release

9YH6 | pdb_00009yh6

Composite structure of the sheathed flagellar motor in Vibrio cholerae adopting a lower FOMC conformation

Literature

In-situ cryo-EM structures reveal mechanisms of sheathed flagellar assembly, rotation, and disassembly in Vibrio cholerae

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)