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8WOE: Cryo-EM structure of the intact flagellar motor-hook complex in the CW state

Analyse 8WOE: Cryo-EM structure of the intact flagellar motor-hook complex in the CW… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8WOE
Type: protein
Length: 80,330 residues
Chains: 451
Method: electron microscopy
Authors: Tan, J.X., Zhang, L., Zhou, Y., Zhu, Y.Q.
Deposited: 10/07/23
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 4.3
Source: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Molecule: Flagellar basal-body rod protein FlgG; Flagellar L-ring protein; Flagellar basal body rod…
UniProt: P0A1J3, P0A1N8, P16437, P26462, P16323, P15928, P0A1L5, P54702, P54700, P0A1I7, P0A1J1, P15930, P26419, P0A1J9, P0A2D5, P26418
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 4.3 · 56 distinct chains · 42% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0, AL, AM, AN	Flagellar basal-body rod protein FlgG	protein	248	24% helix, 32% strand	P0A1J3
1	Flagellar basal-body rod protein FlgG	protein	252	25% helix, 33% strand	P0A1J3
2, 3, 4, 5, 6, 7, 8, 9, ZA, ZB, ZC, ZD, ZE	Flagellar basal-body rod protein FlgG	protein	260	23% helix, 29% strand	P0A1J3
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	Flagellar L-ring protein	protein	211	14% helix, 45% strand	P0A1N8
A0	Flagellar basal body rod protein FlgB	protein	123	59% helix, 4% strand	P16437
A1	Flagellar hook-basal body complex protein FliE	protein	91	85% helix, 0% strand	P26462
A2, A3, A4	Flagellar hook-basal body complex protein FliE	protein	93	82% helix, 0% strand	P26462
A5	Flagellar hook-basal body complex protein FliE	protein	92	85% helix, 1% strand	P26462
A6	Flagellar basal body rod protein FlgB	protein	134	52% helix, 7% strand	P16437
A7	Flagellar basal body rod protein FlgB	protein	121	59% helix, 4% strand	P16437
A8	Flagellar basal body rod protein FlgB	protein	125	56% helix, 4% strand	P16437
A9	Flagellar basal body rod protein FlgB	protein	127	57% helix, 4% strand	P16437
AA	Flagellar basal-body rod protein FlgF	protein	248	28% helix, 31% strand	P16323
AB, AE	Flagellar basal-body rod protein FlgF	protein	249	27% helix, 30% strand	P16323
AC, AD	Flagellar basal-body rod protein FlgF	protein	250	29% helix, 31% strand	P16323
AF, AI	Flagellar basal-body rod protein FlgG	protein	254	25% helix, 30% strand	P0A1J3
AG, AJ	Flagellar basal-body rod protein FlgG	protein	255	25% helix, 30% strand	P0A1J3
AH	Flagellar basal-body rod protein FlgG	protein	256	25% helix, 34% strand	P0A1J3
AK	Flagellar basal-body rod protein FlgG	protein	243	24% helix, 31% strand	P0A1J3
AO, AP, AQ, AR, AS, AT, AU, AV, AW, AX, AY, AZ, Aa, Ac, Ad, Ae, Af, Ag, Ah, Ai, Aj, Ak, Al, Am, An, Ao, Ap, BR, BS, BT, BU, BV, BW, BX	Flagellar M-ring protein	protein	164	26% helix, 43% strand	P15928
Ab, Aq, Ar, As	Flagellar biosynthetic protein FliQ	protein	89	84% helix, 0% strand	P0A1L5
At	Flagellar biosynthetic protein FliR	protein	253	74% helix, 0% strand	P54702
Au	Flagellar biosynthetic protein FliP	protein	207	79% helix, 0% strand	P54700
Av	Flagellar biosynthetic protein FliP	protein	209	80% helix, 0% strand	P54700
Aw, Ax	Flagellar biosynthetic protein FliP	protein	208	77% helix, 1% strand	P54700
Ay	Flagellar biosynthetic protein FliP	protein	209	78% helix, 0% strand	P54700
Az	Flagellar hook-basal body complex protein FliE	protein	59	85% helix, 0% strand	P26462
BA, BC, BD, BE, BF	Flagellar basal-body rod protein FlgC	protein	133	44% helix, 20% strand	P0A1I7
BB	Flagellar basal-body rod protein FlgC	protein	132	44% helix, 18% strand	P0A1I7
BG	Flagellar M-ring protein	protein	13	0% helix, 15% strand	P15928
BH, BJ, BL, BN, BP	Flagellar M-ring protein	protein	16	19% helix, 6% strand	P15928
BI, BO	Flagellar M-ring protein	protein	20	0% helix, 10% strand	P15928
BK, BM, BQ	Flagellar M-ring protein	protein	21	0% helix, 14% strand	P15928
UI, UJ, UK, UL, UM, UN, UO, UP	Flagellar M-ring protein	protein	155	40% helix, 21% strand	P15928
WA	Flagellar M-ring protein	protein	113	35% helix, 20% strand	P15928
WB	Flagellar M-ring protein	protein	111	38% helix, 20% strand	P15928
WC	Flagellar M-ring protein	protein	108	35% helix, 20% strand	P15928
WD	Flagellar M-ring protein	protein	110	39% helix, 20% strand	P15928
WE, WG, WU	Flagellar M-ring protein	protein	112	37% helix, 20% strand	P15928
WF, WQ, WR, WS, WT, WW	Flagellar M-ring protein	protein	111	37% helix, 20% strand	P15928
WH, WI	Flagellar M-ring protein	protein	95	37% helix, 23% strand	P15928
WJ	Flagellar M-ring protein	protein	99	38% helix, 22% strand	P15928
WK	Flagellar M-ring protein	protein	98	39% helix, 22% strand	P15928
WL	Flagellar M-ring protein	protein	85	42% helix, 26% strand	P15928
WM	Flagellar M-ring protein	protein	82	40% helix, 27% strand	P15928
WN	Flagellar M-ring protein	protein	84	40% helix, 26% strand	P15928
WO	Flagellar M-ring protein	protein	96	36% helix, 24% strand	P15928
WP	Flagellar M-ring protein	protein	100	37% helix, 22% strand	P15928
WV	Flagellar M-ring protein	protein	110	37% helix, 20% strand	P15928
ZF, ZG, ZH, ZI, ZJ, ZK, ZL, ZM, ZN, ZO, ZP, ZQ, ZR, ZS, ZT, ZU, ZV, ZW, ZX, ZY, ZZ, Za, Zb, Zc, Zd, Ze, Zf, Zg, Zh	Flagellar hook protein FlgE	protein	401	15% helix, 40% strand	P0A1J1
a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y, z	Flagellar P-ring protein	protein	303	22% helix, 32% strand	P15930
C3, C4, C5, C8, C9, DD, DI, DJ, DK, DM, DN, DO, DP, DQ, DR, DS, DT, DU, DV, DW, Da, Db, Dc, Dg, Dh, Di, Dm, Dn, Do, Ds, Dt, Du, Dy, Dz, D1, D5, D6, D7, EA, EB, B1, B2, B7, B8, B9, EE, EF, EG, EL, EM, EN, ES, ET, EU, EZ, BY, BZ, Be, Bf, Bg, Bl, Bm, Bn, Bs, Bt, Bu, Bz, C1, C2, CD, CE, CF, CK, CL, CM, CR, CS, CT, CY, CZ, Ca, Cf, Cg, Ch, Cm, Cn, Co, Ct, Cu, Cv, FC, FD, FE, FF, FG, FH, FI, FJ, FK, FL, FM, FN	Flagellar motor switch protein FliN	protein	87	24% helix, 51% strand	P26419
C6, DA, DG, DY, De, Dk, Dq, Dw, D3, D9, B5, EC, EJ, EQ, EX, Bc, Bj, Bq, Bx, CB, CI, CP, CW, Cd, Ck, Cr, Cy, Ex, Ey, Ez, E1, E2, E3, E4	Flagellar motor switch protein FliG	protein	310	74% helix, 0% strand	P0A1J9
C7, DB, DH, DZ, Df, Dl, Dr, Dx, D4, D0, B6, ED, EK, ER, EY, Bd, Bk, Br, By, CC, CJ, CQ, CX, Ce, Cl, Cs, Cz, E6, E7, E8, E9, E0, FA, FB	Chemotaxis protein CheY	protein	129	47% helix, 18% strand	P0A2D5
C0, DC, DF, DX, Dd, Dj, Dp, Dv, D2, D8, B4, EI, EP, EW, Bb, Bi, Bp, Bw, CA, CH, CO, CV, Cc, Cj, Cq, Cx, Eq, Er, Es, Et, Eu, Ev, Ew, E5	Flagellar motor switch protein FliM	protein	301	33% helix, 32% strand	P26418
DE, DL, B0, B3, EH, EO, EV, Ba, Bh, Bo, Bv, Ea, CG, CN, CU, Cb, Ci, Cp, Cw, Eb, Ec, Ed, Ee, Ef, Eg, Eh, Ei, Ej, Ek, El, Em, En, Eo, Ep	Flagellar M-ring protein	protein	27	74% helix, 0% strand	P15928

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	723	0.89	0.92	44	empty
2	5499	0.89	0.90	428	empty
3	1162	0.89	0.90	95	empty
4	1065	0.88	0.90	86	empty
5	3234	0.88	0.90	255	empty

Interfaces

1,802 interfaces between chains.

q–r · 3605 Å² buried · 52 hydrogen bonds · protein-protein
e–f · 3603 Å² buried · 52 hydrogen bonds · protein-protein
k–l · 3603 Å² buried · 52 hydrogen bonds · protein-protein
o–p · 3603 Å² buried · 52 hydrogen bonds · protein-protein
i–j · 3598 Å² buried · 52 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 26 disulfide (disulfide).

Compared structures

P0A1J3 · AlphaFold monomer V2.0 prediction for flagellar basal-body rod protein flgg (P0A1J3) · a predicted model of the same protein · chain 7 against A, TM-score 0.97

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P0A1J3
Every structure of UniProt P0A1N8
Every structure of UniProt P16437
Every structure of UniProt P26462
Every structure of UniProt P16323
Every structure of UniProt P15928
Every structure of UniProt P0A1L5
Every structure of UniProt P54702
Every structure of UniProt P54700
Every structure of UniProt P0A1I7
Every structure of UniProt P0A1J1
Every structure of UniProt P15930
Every structure of UniProt P26419
Every structure of UniProt P0A1J9
Every structure of UniProt P0A2D5
Every structure of UniProt P26418
Elsewhere: RCSB PDB 8WOE · PDBe 8WOE · UniProt P0A1J3 · UniProt P0A1N8 · UniProt P16437 · UniProt P26462 · UniProt P16323 · UniProt P15928 · UniProt P0A1L5 · UniProt P54702 · UniProt P54700 · UniProt P0A1I7 · UniProt P0A1J1 · UniProt P15930 · UniProt P26419 · UniProt P0A1J9 · UniProt P0A2D5 · UniProt P26418

Other records of 8WOE

8WOE-2 · MolNFT · Cryo-EM structure of the intact flagellar motor-hook complex in the CW state
8WOE-3 · MolNFT · Cryo-EM structure of the intact flagellar motor-hook complex in the CW state
8WOE-4 · MolNFT · Cryo-EM structure of the intact flagellar motor-hook complex in the CW state
8WOE-5 · MolNFT · Cryo-EM structure of the intact flagellar motor-hook complex in the CW state
8WOE-6 · MolNFT · Cryo-EM structure of the intact flagellar motor-hook complex in the CW state

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