9yh6
Composite structure of the sheathed flagellar motor in Vibrio cholerae adopting a lower FOMC conformation
Method: ELECTRON MICROSCOPY
Dmax: 465.8 Å
Quality: GOOD
SAXS Profile
P(r) Distribution
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1. Structure Basics
| entry_id | 9yh6 |
| deposition_date | 2025-09-30 |
| title | Composite structure of the sheathed flagellar motor in Vibrio cholerae adopting a lower FOMC conformation |
| keywords | In situ cryo-EM, Vibrio cholerae, flagellar motor, assembled state., MOTOR PROTEIN; MOTOR PROTEIN |
| method | ELECTRON MICROSCOPY |
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Download Data
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2. SAXS Parameters (CRYSOL)
| rg_guinier | — Å |
| rg_electron | 150.20 Å |
| i0 | 952858000000.00 |
| molecular_weight | 8178100.0 kDa |
| excluded_volume | 10160000 ų |
| envelope_volume | 18362000 ų |
| shell_volume | 938960 ų |
| envelope_diameter | 465.3 Å |
| shell_rg | 158.90 Å |
| envelope_rg | 149.70 Å |
| shape_rg | 150.20 Å |
| total_rg | 150.20 Å |
| total_atoms | 574924 |
| n_residues | 73994 |
| n_harmonics | 20 |
| q_range | — – 0.5000 Å−1 |
| n_points | 101 |
| shell_type | directional |
| solvent_density | 0.3340 e/ų |
| contrast_shell | 0.0300 e/ų |
| crysol_version | 4.1.3 |
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3. P(r) Analysis (GNOM)
| dmax | 465.8 Å |
| rg_real | 151.30 Å |
| rg_real_error | 2.03 Å |
| i0_real | 9.2910e+11 |
| i0_real_error | 2.4110e+10 |
| rg_reciprocal | 153.40 Å |
| i0_reciprocal | 957000000000.0000 |
| total_estimate | 0.8924 |
| solution_quality | GOOD a GOOD solution |
| n_peaks | 1 |
| r_peak_primary | 186.3 Å |
| skewness | 0.231 |
| kurtosis | -0.463 |
| angular_range | — – 0.0500 Å−1 |
| current_alpha | 1.7650 |
| highest_alpha | 38820000000.0000 |
| n_real_points | 11 |
| gnom_version | 4.1.3 |
| quality_criteria | AN1: 0.000; Oscil: 0.964; Stabil: 0.926; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.000 |
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4. Crystallography & Experiment
Unit Cell
| length_a | 1.000 Å |
| length_b | 1.000 Å |
| length_c | 1.000 Å |
| angle_alpha | 90.00 ° |
| angle_beta | 90.00 ° |
| angle_gamma | 90.00 ° |
| z_pdb | — |
Symmetry
| space_group | P 1 |
| int_tables_number | 1 |
| crystal_system | triclinic |
EM 3D
| resolution | 3.60 Å |
| resolution_method | — |
| num_particles | 53628 |
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5. Entities & Polymer Info (13)
Entity 1 polymer
| description | Flagellar basal-body rod protein FlgG |
| formula_weight | 28114.3 kDa |
| src_method | man |
| entity_count | 27 |
Polymer
| type | polypeptide(L) |
| strand_id | Aa,Ab,Ac,Ad,Ae,Af,Ag,Ah,Ai,Aj,Ak,Al,Am,An,Ao,Ap,Aq,Ar,As,At,Au,Av,Aw,Ax,Ay,Az,Bb |
| atom_count | 574924 |
MQPALWVSKTGLDAQQTNIATISNNLANASTIGFKKGRAVFEDLFYQNINQPGAQSSQNTRLPSGLMLGAGSKVVATQKVHTNGNVQTTSNSLDMMIEGDGFFQILMPDGNIAYSRNGQFTLDDEGAIVTSGAGYRLQPEIIIPEDAISITIGNDGEVSVRVRGQQDNQVLGQITTVDFINPGGLEPVGQNLYLPTGASGEPQEGVPGLDGLGDIRQSMLETSNVNVTEELVNMIEAQRVYEMNSKVISAVDKMMSFVNQQL
Source
| organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
| ncbi_taxonomy_id | 243277 |
| host_organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
Entity 2 polymer
| description | Flagellar basal-body rod protein FlgF |
| formula_weight | 26778.3 kDa |
| src_method | man |
| entity_count | 5 |
Polymer
| type | polypeptide(L) |
| strand_id | Ba,Bc,Bd,Bv,Bw |
MDRALFLAMSGAKQNMQAMQLRANNLANVSTTGFRADLAQARSMQAYGEGLPSRVFSMTERPGHNFAQGSVITTGRDLDITIQGDGWISVLDKTGKEGLTRNGNLRIDETGLLLNGNGHPVLGETGAPITLPVPLNKVEIGGDGTISVRPQGAPADAMEVVDRIKLVRLNDQSLFKDVNGLFRATDPNTQFEADASVKILTGALEGSNVNAIGEMTSLIDLQRQFEMQVKMMSTAEEMDKASDSLLRSS
Source
| organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
| ncbi_taxonomy_id | 243277 |
| host_organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
Entity 3 polymer
| description | Flagellar hook protein FlgE |
| formula_weight | 46880.3 kDa |
| src_method | man |
| entity_count | 17 |
Polymer
| type | polypeptide(L) |
| strand_id | Be,Bf,Bg,Bh,Bi,Bj,Bk,Bl,Bm,Bn,Bo,Bp,Bq,Br,Bs,Bt,Bu |
MSYVSLSGLSAAQMDLNTTSNNIANANTFGFKESRAEFGDVYSTSLFTNAKTTPGQGVQAAKVAQQFHEGSSIYTNNPLDLRIAGTGFFAVAKDRLVPQQNELTRNGAFHLDKNSFMVTANDEFLLGYEVNPDTGDVLSYEPKPINIPPQFGKPKQTANIDLGANLPANGDLKDPALFDITDPETYNRTTSSTIYDSMGQPYKLTTYYLKDMNQANTWQTYYTVTDKTGEKPINVVGGDAASPTGHVGHTMRFNNDGTLSSLNNGQPIVTEPLGGGANPVDLNGADVNQTLSFSLDSATQFAAPFELTKFDQDGATTGFLTKIDFDENGSVLATYSNGINTTLGRVALVRVANEQGLDKKGGTQWDATQFSGAKIWGESNKGSFGSISNGSLEQSNIDMTQELVDLISAQRNFQANSRALEVHNGLQQNILQIR
Source
| organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
| ncbi_taxonomy_id | 243277 |
| host_organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
Entity 4 polymer
| description | Flagellar L-ring protein |
| formula_weight | 24256.5 kDa |
| src_method | man |
| entity_count | 26 |
Polymer
| type | polypeptide(L) |
| strand_id | Bx,By,Bz,Ca,Cb,Cc,Cd,Ce,Cf,Cg,Ch,Ci,Cj,Ck,Cl,Cm,Cn,Co,Cp,Cq,Cr,Cs,Ct,Cu,Cv,Cw |
TTTVDAVEGDKSESNSGLTDALRNRTDPVAGDPAWAPIHPKGKPEHYAAETGSLFNLASSSSMYDDSKPRGVGDIITVTLNESTKAAKSADADLNKKNDASMDPLAVGGKDLTIGDYNFSYALKNDNKFSGSAAANQSNSMSGSITVEVIEVLANGNLVIRGEKWLTLNTGDEYIRLSGTIRPDDIDFDNTIASNRISNARIQYSGTGTNQDMQEPGFLARFFNVSL
Source
| organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
| ncbi_taxonomy_id | 243277 |
| host_organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
Entity 5 polymer
| description | Flagellar P-ring protein |
| formula_weight | 35702.6 kDa |
| src_method | man |
| entity_count | 26 |
Polymer
| type | polypeptide(L) |
| strand_id | Cx,Cy,Cz,Da,Db,Dc,Dd,De,Df,Dg,Dh,Di,Dj,Dk,Dl,Dm,Dn,Do,Dp,Dq,Dr,Ds,Dt,Du,Dv,Dw |
ARIKDVAQVAGVRNNQLVGYGLVTGLPGTGESTPFTDQSFNAMLQSFGIQLPPGTKPKTKNVAAVIVTADLPAFSKQGQTIDITVSSIGSAKSLRGGTLMQTFLKGLDGQVYAVAQGNLVVSGFSATGADGSKIVGNNPTVGMISSGAIVEREVPNPFGRGDYITFNLFESDFTTAQRLADAVNQFLGPQMASAVDAASIKVRAPRDLSQRVAFLSAIENLEFNPADSAAKIIVNSRTGTIVVGQNVRLKPAAVTHGGMTVAIKENLNVSQPNALGGGQTVVVPNTEIEVTEKQGKMFKLEPGVTLDDLVRAVNEVGAAPSDLMAILQALKQAGAIEGQLIII
Source
| organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
| ncbi_taxonomy_id | 243277 |
| host_organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
Entity 6 polymer
| description | Flagellar protein FlgT |
| formula_weight | 39808.2 kDa |
| src_method | man |
| entity_count | 26 |
Polymer
| type | polypeptide(L) |
| strand_id | Dx,Dy,Dz,Ea,Eb,Ec,Ed,Ee,Ef,Eg,Eh,Ei,Ej,Ek,El,Em,En,Eo,Ep,Eq,Er,Es,Et,Eu,Ev,Ew |
YEVTGSAAIVSSEEVARLHALEDALYKAVNFAGADIGSISNLMPLLESDRREYLFANHEVRYILIEERKAINNVMYVRTRIDIYPSATACHVEQYKKTMLIGNIDLASPQQAVMGQIYQVGDDFAQVINRRLEQESRSFVSVGTTQYDIDPKAPERIKMIAQDAGAQYIMGGMITDLTATIEQKTLQDDIINRQFAMEISVFDGKTGNEVMTRTYREVARWPFPKTSQIDTRSARFWASTYGEMMLRVSRNIMLDLESEISCKITLPQIVAKFGTTATMDLGRIHGVKQGDKLSLWHTGAFIDQQGLPRNKVTQSEITLTVSRVYEHEAELTVDQPELAYSIQIGDVMHKQM
Source
| organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
| ncbi_taxonomy_id | 243277 |
| host_organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
Entity 7 polymer
| description | Sodium-type flagellar protein MotY |
| formula_weight | 31208.0 kDa |
| src_method | man |
| entity_count | 26 |
Polymer
| type | polypeptide(L) |
| strand_id | Ex,Ey,Ez,Fa,Fb,Fc,Fd,Fe,Ff,Fg,Fh,Fi,Fj,Fk,Fl,Fm,Fn,Fo,Fp,Fq,Fr,Fs,Ft,Fu,Fv,Fw |
LEVRYMATPQQSTWQMATNTPLECRLVHPIPNYGDAEFSSRAGKKINLDFELKMRRPMGDTRNVSLVSMPPVWRPGEGADRITNLQFFKQFDGYIGGQTAWSLLSELEKGRYPTFSYQDWQSRDQRIEVALSSVLFQQPYNEFSDCISKLLPYSFEDISFTILHYDQGTSVELNKASQKRLAQIAEYVRYNQDIDLVLVSTYTDSTDTNNNSQNLSEQRAEVLREYFKSIGLPEDRIQVQGYGKRRPIADNASPIGKDKNRRVVISLGRTQ
Source
| organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
| ncbi_taxonomy_id | 243277 |
| host_organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
Entity 8 polymer
| description | Sodium-type flagellar protein MotX |
| formula_weight | 21244.1 kDa |
| src_method | man |
| entity_count | 26 |
Polymer
| type | polypeptide(L) |
| strand_id | Fx,Fy,Fz,Ga,Gb,Gc,Gd,Ge,Gf,Gg,Gh,Gi,Gj,Gk,Gl,Gm,Gn,Go,Gp,Gq,Gr,Gs,Gt,Gu,Gv,Gw |
PVPIYSEAELIKLIEENKHLERVKADNCQIVEDIVARATRISLPSYEFLYGDMLAWGVCVDQDVELGLYYMENAAHQGLPAALEQLGRYYSRGTLVQQDKERAIPYLREAAAMGNLNARIQLAELLLRDYGSPLDYEDAYRWLYNSVTADQRTHNRIALLRQGLERRMPENIIARAKRRETFW
Source
| organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
| ncbi_taxonomy_id | 243277 |
| host_organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
Entity 9 polymer
| description | FlgP |
| formula_weight | 1506.8 kDa |
| src_method | man |
| entity_count | 52 |
Polymer
| type | polypeptide(L) |
| strand_id | ;Gx,Gy,Gz,Ha,Hb,Hc,Hd,He,Hf,Hg,Hh,Hi,Hj,Hk,Hl,Hm,Hn,Ho,Hp,Hq,Hr,Hs,Ht,Hu,Hv,Hw,Hx,Hy,Hz,Ia,Ib,Ic,Id,Ie,If,Ig,Ih,Ii,Ij,Ik,Il,Im,In,Io,Ip,Iq,Ir,Is,It,Iu,Iv,Iw ; |
QQVPEKRQMTLF
Source
| organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
| ncbi_taxonomy_id | 243277 |
| host_organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
Entity 10 polymer
| description | Chemotaxis protein PomB |
| formula_weight | 17542.8 kDa |
| src_method | man |
| entity_count | 26 |
Polymer
| type | polypeptide(L) |
| strand_id | Ix,Iy,Iz,Ja,Jb,Jc,Jd,Je,Jf,Jg,Jh,Ji,Jj,Jk,Jl,Jm,Jn,Jo,Jp,Jq,Jr,Js,Jt,Ju,Jv,Jw |
QQQAQAMSEQMETVAESIKKALSREIEQGAIEVENLGQQIDIRIREKGAFPEGSAFLQPKFRPLVRQIAELVKDIPGKVRVTGHTDNQKLDSELYRSNWDLSAQRAVSVAQEMEKVKDFDHLRLQVRGLADTQPLGPNDTEAQRATNRRVEISIL
Source
| organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
| ncbi_taxonomy_id | 243277 |
| host_organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
Entity 11 polymer
| description | Lipoprotein |
| formula_weight | 11947.4 kDa |
| src_method | man |
| entity_count | 58 |
Polymer
| type | polypeptide(L) |
| strand_id | ;Jx,Jy,Jz,Ka,Kb,Kc,Kd,Ke,Kf,Kg,Kh,Ki,Kj,Kk,Kl,Km,Kn,Ko,Kp,Kq,Kr,Ks,Kt,Ku,Kv,Kw,Kx,Ky,Kz,La,Lb,Lc,Ld,Le,Lf,Lg,Lh,Li,Lj,Lk,Ll,Lm,Ln,Lo,Lp,Lq,Lr,Ls,Lt,Lu,Lv,Lw,Lx,Ly,Lz,Ma,Mb,Mc ; |
PDDWLTAVGYANISEQRGRDEAEKQVRAMRASKIDAYRELAEQVYGMRISGRAELQDQRLGTELTAGAVDGVIRGAEVVRSYKVGDSYVTELRLDIRKMDKMRDY
Source
| organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
| ncbi_taxonomy_id | 243277 |
| host_organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
Entity 12 polymer
| description | FlgO domain-containing protein |
| formula_weight | 21395.1 kDa |
| src_method | man |
| entity_count | 58 |
Polymer
| type | polypeptide(L) |
| strand_id | ;Md,Me,Mf,Mg,Mh,Mi,Mj,Mk,Ml,Mm,Mn,Mo,Mp,Mq,Mr,Ms,Mt,Mu,Mv,Mw,Mx,My,Mz,Na,Nb,Nc,Nd,Ne,Nf,Ng,Nh,Ni,Nj,Nk,Nl,Nm,Nn,No,Np,Nq,Nr,Ns,Nt,Nu,Nv,Nw,Nx,Ny,Nz,Oa,Ob,Oc,Od,Oe,Of,Og,Oh,Oi ; |
IYNGKEPYNGSQFMLMESPRHTLDFFVESMTEDLMLSNTSITARTPIAVTSFVDLQNMDTTNWLGNSVSEGFIHQFQRRGFKVVDFKTTGSIQVTQQGDFAFSRDWKNLSSEQEVQYVLTGTMLRQEGGVIVNARVVGMHSRIVVATAQGFLPADRIGRDLDTLNSIRTQDGVLIRSDPTITQPYTVILR
Source
| organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
| ncbi_taxonomy_id | 243277 |
| host_organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
Entity 13 polymer
| description | FliF |
| formula_weight | 16142.0 kDa |
| src_method | man |
| entity_count | 34 |
Polymer
| type | polypeptide(L) |
| strand_id | Oj,Ok,Ol,Om,On,Oo,Op,Oq,Or,Os,Ot,Ou,Ov,Ow,Ox,Oy,Oz,Pa,Pb,Pc,Pd,Pe,Pf,Pg,Ph,Pi,Pj,Pk,Pl,Pm,Pn,Po,Pp,Pq |
VSAARRKEQELEKQQEEALRGKIDSVLIPILGLGNYTAQVDIELDFSAVEQTRKVFDPNTPATRSEYTLEDYNVHKEATRNYELDTTISHERKQSGVINRQTVAVAVKSLSEADLNSIRQVLIGTVGYSENRGDLLNVLSMPFA
Source
| organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
| ncbi_taxonomy_id | 243277 |
| host_organism | Vibrio cholerae O1 biovar El Tor str. N16961 |
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6. Citations (1)
In-situ cryo-EM structures reveal mechanisms of sheathed flagellar assembly, rotation, and disassembly in Vibrio cholerae
To Be Published
PRIMARY
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7. Files & Curves (10)
Files (7)
- pr_distribution /app/data/pr_computation/yh/9yh6/pr_distribution.json
- pr_output /app/data/pr_computation/yh/9yh6/9yh6.pr.out
- pr_plot /app/data/visualization/pr_computation/yh/9yh6/9yh6_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/yh/9yh6/9yh6.dat
- saxs_fit /app/data/saxs_computation/yh/9yh6/9yh6.fit
- saxs_log /app/data/saxs_computation/yh/9yh6/9yh6.log
- saxs_plot /app/data/visualization/saxs_computation/yh/9yh6/9yh6_saxs_profile.png
Curves (3)
| fit | /app/data/saxs_computation/yh/9yh6/9yh6.fit |
| pddf | /app/data/pr_computation/yh/9yh6/9yh6.pr.out |
| profile | /app/data/saxs_computation/yh/9yh6/9yh6.dat |