SMTL ID : 8b6j.1

Cryo-EM structure of cytochrome bc1 complex (complex-III) from respiratory supercomplex of Tetrahymena thermophila

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-mer

Ligands

15 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.1: 23 residues within 4Å: Chain A: W.504, Y.505, G.506, N.507, T.508 Chain C: M.1, E.2, W.3, F.121, L.124, V.128 Chain G: P.183, L.184, M.186, F.187 Chain K: Y.21, Y.24, L.28 Ligands: PC1.19, PC1.23, CDL.27, PC1.28, CDL.31 6 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C, 2 interactions with chain K pi-Cation interactions: A:W.504 Hydrophobic interactions: C:F.121, K:Y.21, K:Y.24 Hydrogen bonds: C:M.1, C:W.3 PC1.2: 21 residues within 4Å: Chain A: A.403, S.404, T.468, W.472, Y.505 Chain B: F.30, I.31, Y.32 Chain I: Y.61, Y.62, P.63, F.64, L.65 Chain K: F.16, K.19, R.20, V.22, G.23, G.25, P.26, L.29 13 PLIP interactions: 2 interactions with chain I, 3 interactions with chain A, 5 interactions with chain K, 3 interactions with chain B Hydrophobic interactions: I:F.64, K:V.22, K:P.26, K:L.29, B:F.30, B:F.30 pi-Cation interactions: I:Y.62, A:W.472, A:W.472, B:Y.32 Hydrogen bonds: A:S.404 Salt bridges: K:K.19, K:R.20 PC1.9: 24 residues within 4Å: Chain C: V.17, W.222, F.223, D.224, L.227, L.231 Chain L: D.473, R.495, R.499, L.502 Chain P: Y.93, N.96, Y.100, L.103, L.104, A.107 Chain T: Q.60, P.63, W.66, Q.67, I.70 Ligands: CDL.6, UQ8.13, CDL.24 11 PLIP interactions: 2 interactions with chain C, 4 interactions with chain P, 3 interactions with chain L, 2 interactions with chain T Hydrophobic interactions: C:F.223, C:L.227, P:L.103, P:L.104 Hydrogen bonds: P:Y.100, T:Q.67 pi-Cation interactions: P:Y.93, T:W.66 Salt bridges: L:D.473, L:R.495, L:R.499 PC1.10: 30 residues within 4Å: Chain C: I.93, Y.96, F.97, F.100, Y.249, Y.257, W.280, R.283, P.284, F.285, W.288, G.301, L.302, Y.305, A.366, L.367, V.369, T.370, S.371, Y.372, F.392, I.395, F.396 Chain O: F.25, Y.27, W.35, G.36, I.37 Ligands: CDL.7, CDL.21 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain O Hydrophobic interactions: C:I.93, C:Y.96, C:Y.96, C:Y.96, C:F.100, C:W.280, C:F.285, C:F.285, C:Y.305, C:T.370, C:F.392, C:F.392, C:I.395, C:F.396, C:F.396 Hydrogen bonds: C:Y.249 Salt bridges: C:R.283 pi-Cation interactions: O:W.35, O:W.35 PC1.11: 33 residues within 4Å: Chain C: L.40, T.41, A.43, S.44, V.47, W.82, L.83, R.86, G.87, M.90, M.234, I.238, V.241, M.242, I.243, C.245, F.246, F.247, Y.249, S.256, E.258 Chain O: M.254, Y.257, Y.258, F.261 Chain P: F.106, A.107, Y.110, A.111 Ligands: CDL.7, CDL.21, CDL.24, PC1.35 11 PLIP interactions: 8 interactions with chain C, 2 interactions with chain O, 1 interactions with chain P Hydrophobic interactions: C:L.83, C:R.86, C:M.242, C:F.246, C:F.246, O:Y.257, O:F.261, P:Y.110 Hydrogen bonds: C:W.82 Salt bridges: C:R.86, C:E.258 PC1.18: 38 residues within 4Å: Chain D: D.252, R.256, Y.257, M.259, V.260, F.261, G.263, G.264, I.267 Chain E: G.102, L.103, S.105, F.106, L.109, Y.110, M.112, G.113, P.263, Q.265, R.266, F.267, W.268 Chain I: W.77, F.78, C.81, Y.82 Chain N: L.75, Y.76, D.79, F.80, W.82, L.83, I.235, I.238, L.239, M.242 Ligands: PC1.28, PC1.29 20 PLIP interactions: 4 interactions with chain D, 2 interactions with chain I, 8 interactions with chain N, 6 interactions with chain E Hydrophobic interactions: D:Y.257, D:Y.257, D:V.260, D:I.267, I:F.78, N:Y.76, N:W.82, N:L.83, N:I.235, N:I.235, N:I.238, N:I.238, N:L.239, E:F.106, E:F.106, E:F.106, E:L.109 Hydrogen bonds: I:Y.82, E:W.268 pi-Cation interactions: E:W.268 PC1.19: 27 residues within 4Å: Chain C: Y.153, G.161, K.162, F.163, W.165, W.166 Chain E: A.111, V.114, I.115, L.118, N.119, G.120, W.121, K.122 Chain K: S.32, L.36, A.39, L.40, N.42, M.43 Ligands: PC1.1, PEE.14, CDL.27, PC1.28, PC1.29, CDL.31, UQ8.32 12 PLIP interactions: 2 interactions with chain K, 3 interactions with chain E, 7 interactions with chain C Hydrophobic interactions: K:A.39, E:A.111, E:I.115, E:L.118, C:F.163, C:F.163, C:F.163, C:W.166 Hydrogen bonds: K:N.42, C:K.162 pi-Cation interactions: C:W.165, C:W.165 PC1.23: 19 residues within 4Å: Chain A: W.504 Chain C: W.3, I.303, Y.304, F.307, Y.311 Chain G: W.175, L.184, M.186, F.187, Y.189 Chain K: N.14, R.17, L.18, Y.21 Ligands: PC1.1, CDL.8, CDL.27, PEE.43 9 PLIP interactions: 2 interactions with chain K, 5 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: K:L.18, C:I.303, C:F.307, C:F.307, C:F.307 Salt bridges: K:R.17 pi-Cation interactions: C:W.3, G:W.175, G:W.175 PC1.28: 30 residues within 4Å: Chain A: D.473, R.495, R.499, L.502 Chain E: Y.93, N.96, Y.100, L.103, L.104, F.106, A.107 Chain I: Q.60, P.63, W.66, Q.67, I.70 Chain K: L.28 Chain N: L.40, F.223, D.224, L.227, L.231, M.234, I.235, I.238 Ligands: PC1.1, PC1.18, PC1.19, CDL.27, PC1.29 17 PLIP interactions: 4 interactions with chain N, 2 interactions with chain A, 9 interactions with chain E, 2 interactions with chain I Hydrophobic interactions: N:L.40, N:M.234, N:I.235, N:I.238, E:Y.100, E:Y.100, E:L.103, E:L.104, E:F.106, E:F.106 Salt bridges: A:R.495, A:R.499 Hydrogen bonds: E:N.96, E:Y.100, I:Q.67 pi-Cation interactions: E:Y.93, I:W.66 PC1.29: 34 residues within 4Å: Chain D: R.250, M.254, Y.257, Y.258, F.261 Chain E: F.106, A.107, Y.110 Chain N: L.40, T.41, S.44, W.82, L.83, R.86, G.87, D.89, M.90, M.234, I.238, V.241, M.242, I.243, C.245, F.246, F.247, Y.249, E.258 Ligands: PC1.18, PC1.19, CDL.27, PC1.28, CDL.33, PC1.34, CDL.40 14 PLIP interactions: 4 interactions with chain D, 1 interactions with chain E, 9 interactions with chain N Hydrophobic interactions: D:Y.257, D:Y.258, D:F.261, D:F.261, E:Y.110, N:T.41, N:M.242, N:I.243, N:F.246, N:F.246, N:F.247 Hydrogen bonds: N:W.82 Salt bridges: N:R.86 pi-Cation interactions: N:Y.249 PC1.30: 26 residues within 4Å: Chain N: V.128, Y.153, G.161, K.162, F.163, W.165, W.166, L.184, L.188 Chain P: I.115, L.118, N.119, G.120, W.121, K.122, H.261 Chain V: L.29, S.32, I.33, L.36, A.39, L.40, N.42, M.43 Ligands: CDL.6, CDL.24 6 PLIP interactions: 3 interactions with chain N, 3 interactions with chain V Hydrophobic interactions: N:W.166, N:W.166, V:I.33, V:A.39 pi-Cation interactions: N:W.165 Hydrogen bonds: V:N.42 PC1.34: 33 residues within 4Å: Chain D: F.25, I.26, Y.27, W.35, G.36, I.37 Chain N: I.93, Y.96, F.97, F.100, Y.249, Y.257, W.280, R.283, P.284, F.285, W.288, G.301, L.302, Y.305, A.366, L.367, V.369, T.370, S.371, Y.372, F.392, I.395, F.396 Chain S: Y.108, C.112 Ligands: PC1.29, CDL.33 21 PLIP interactions: 16 interactions with chain N, 4 interactions with chain D, 1 interactions with chain S Hydrophobic interactions: N:Y.96, N:Y.96, N:Y.96, N:Y.96, N:F.97, N:F.100, N:F.285, N:W.288, N:L.302, N:A.366, N:L.367, N:I.395, N:F.396, D:F.25, D:I.26, S:Y.108 Hydrogen bonds: N:Y.249 Salt bridges: N:R.283, N:R.283 pi-Cation interactions: D:W.35, D:W.35 PC1.35: 36 residues within 4Å: Chain C: L.75, Y.76, D.79, F.80, W.82, L.83, I.235, I.238, L.239, M.242 Chain O: D.252, R.256, Y.257, M.259, V.260, F.261, G.263, G.264, I.267 Chain P: G.102, L.103, S.105, F.106, L.109, Y.110, M.112, G.113, Q.265, R.266, F.267, W.268 Chain T: W.77, F.78, C.81, Y.82 Ligands: PC1.11 15 PLIP interactions: 5 interactions with chain P, 6 interactions with chain O, 3 interactions with chain C, 1 interactions with chain T Hydrophobic interactions: P:F.106, P:F.106, P:F.106, O:R.256, O:Y.257, O:V.260, O:V.260, O:V.260, C:Y.76, C:I.235, C:L.239 Hydrogen bonds: P:W.268, T:Y.82 pi-Cation interactions: P:W.268 Salt bridges: O:R.256 PC1.39: 17 residues within 4Å: Chain R: I.7, W.9, N.14, R.20, R.22, F.193, W.198, D.199, F.201, Y.208 Chain W: P.3, V.4, F.5, L.6, L.9, V.12 Ligands: CDL.38 15 PLIP interactions: 7 interactions with chain R, 8 interactions with chain W Hydrophobic interactions: R:W.9, R:F.193, W:F.5, W:F.5, W:F.5, W:F.5, W:L.6 Hydrogen bonds: R:W.9, R:N.14, W:V.4, W:F.5, W:L.6 Salt bridges: R:R.20, R:D.199 pi-Cation interactions: R:Y.208 PC1.42: 18 residues within 4Å: Chain L: A.403, S.404, T.468, W.472, Y.505 Chain M: F.30, I.31, Y.32 Chain T: Y.61, Y.62, P.63, F.64 Chain V: F.16, K.19, R.20, V.22, G.23, P.26 15 PLIP interactions: 5 interactions with chain L, 4 interactions with chain V, 4 interactions with chain M, 2 interactions with chain T Hydrogen bonds: L:S.404, L:S.404, L:Y.505, V:G.23 pi-Cation interactions: L:W.472, L:W.472, M:Y.32 Hydrophobic interactions: V:V.22, V:P.26, M:F.30, M:F.30, M:I.31, T:Y.62, T:F.64 Salt bridges: V:R.20

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.3: 29 residues within 4Å: Chain C: I.42, Q.45, L.46, G.49, T.50, L.52, A.53, L.56, R.67, F.81, H.84, E.85, V.88, L.91, F.126, V.129, V.130, G.133, L.134, L.136, C.137, H.185, Y.186, A.189, F.190, L.192, H.279, Y.281 Ligands: UQ8.12 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:Q.45, C:L.52, C:A.53, C:L.56, C:V.88, C:F.126, C:V.129, C:V.130, C:V.130, C:Y.186, C:Y.186, C:Y.186, C:A.189, C:L.192 Hydrogen bonds: C:E.85 Salt bridges: C:R.67, C:H.279 Metal complexes: C:H.84, C:H.185 HEM.4: 29 residues within 4Å: Chain C: S.32, L.33, G.35, F.36, T.38, F.39, I.42, L.91, S.95, H.98, L.99, K.102, N.107, Q.112, A.115, W.116, G.119, V.120, T.122, F.123, F.126, L.192, G.196, H.199, M.203, D.206, W.207, K.208 Ligands: UQ8.13 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:T.38, C:L.99, C:K.102, C:A.115, C:W.116, C:W.116, C:V.120, C:T.122, C:F.123, C:M.203 Hydrogen bonds: C:G.35, C:N.107, C:W.207, C:K.208 Salt bridges: C:H.98, C:K.102, C:K.208 Metal complexes: C:H.199 HEM.25: 29 residues within 4Å: Chain N: I.42, Q.45, L.46, G.49, T.50, L.52, A.53, L.56, R.67, F.81, H.84, E.85, V.88, L.91, F.126, V.129, V.130, G.133, L.134, L.136, C.137, H.185, Y.186, A.189, F.190, L.192, H.279, Y.281 Ligands: UQ8.12 22 PLIP interactions: 22 interactions with chain N, Hydrophobic interactions: N:Q.45, N:L.52, N:A.53, N:L.56, N:L.56, N:F.81, N:V.88, N:F.126, N:V.129, N:V.130, N:V.130, N:L.136, N:L.136, N:Y.186, N:Y.186, N:A.189, N:L.192 Hydrogen bonds: N:E.85 Salt bridges: N:R.67, N:H.279 Metal complexes: N:H.84, N:H.185 HEM.26: 30 residues within 4Å: Chain N: S.32, L.33, F.34, G.35, F.36, T.38, F.39, I.42, L.91, S.95, H.98, L.99, K.102, N.107, Q.112, A.115, W.116, G.119, V.120, T.122, F.123, F.126, G.196, H.199, M.203, D.206, W.207, K.208, L.309 Ligands: UQ8.32 17 PLIP interactions: 17 interactions with chain N, Hydrophobic interactions: N:T.38, N:L.99, N:K.102, N:W.116, N:W.116, N:V.120, N:T.122, N:F.123, N:M.203 Hydrogen bonds: N:G.35, N:Q.112, N:W.207, N:K.208, N:K.208 Salt bridges: N:H.98, N:K.102 Metal complexes: N:H.199

15 x CDL: CARDIOLIPIN(Non-covalent)

CDL.5: 28 residues within 4Å: Chain C: R.327, V.329, A.330, F.331, V.332, F.335, I.341, L.354, I.357, T.358, L.361, W.390, Y.394, F.397, F.403, L.404, P.407, L.408, I.409 Chain G: F.51, S.52, I.55, L.56 Chain X: Y.14, S.15, L.18, Y.19, Y.22 14 PLIP interactions: 7 interactions with chain C, 5 interactions with chain G, 2 interactions with chain X Hydrophobic interactions: C:F.331, C:V.332, G:F.51, G:F.51, G:I.55, G:I.55, G:L.56, X:L.18 Hydrogen bonds: C:A.330, C:F.331, C:V.332, C:L.408, C:I.409, X:Y.14 CDL.6: 36 residues within 4Å: Chain C: T.11, S.12, I.13, I.16, F.39, A.43, L.46, V.47, T.50, V.187, F.190, A.193, Y.194, L.197 Chain N: T.7, T.11, F.121, W.166, L.184, V.187, L.188, F.190, F.191, Y.194, L.195, I.198 Chain R: K.180, I.181, T.182, P.183 Ligands: PC1.9, UQ8.12, UQ8.13, CDL.24, PC1.30, CDL.31 18 PLIP interactions: 5 interactions with chain N, 10 interactions with chain C, 3 interactions with chain R Hydrophobic interactions: N:L.184, N:V.187, N:L.188, N:F.191, N:Y.194, C:I.13, C:I.16, C:A.43, C:L.46, C:F.190, C:A.193 Hydrogen bonds: C:T.11, C:S.12, C:S.12, C:I.13, R:I.181, R:T.182 Salt bridges: R:K.180 CDL.7: 44 residues within 4Å: Chain C: D.29, I.30, N.31, F.34, R.86, D.89, M.90, I.93, F.97, F.100, R.101, Y.104, L.105, E.210, I.237, I.240, V.241, V.244, C.245, M.248, Y.249, W.280, E.350, F.359, W.360, L.363, C.364, L.367 Chain G: R.130 Chain H: V.91, W.92, R.95, N.96, I.97, T.99, F.100, V.104, L.105, Y.108 Chain O: F.25, W.35 Ligands: PC1.10, PC1.11, CDL.21 25 PLIP interactions: 12 interactions with chain C, 8 interactions with chain H, 2 interactions with chain O, 3 interactions with chain G Hydrophobic interactions: C:D.89, C:F.97, C:F.100, C:I.240, C:V.241, C:V.244, C:F.359, C:L.367, H:W.92, H:I.97, H:F.100, H:V.104, H:Y.108, H:Y.108, O:F.25, O:F.25 Hydrogen bonds: C:N.31, C:Y.104, H:R.95, H:N.96, G:R.130, G:R.130 Salt bridges: C:R.101, C:R.101, G:R.130 CDL.8: 30 residues within 4Å: Chain C: F.156, L.299, F.300, I.303, Y.304, F.307, I.308, Y.311, V.314, I.315, T.325, R.327, N.328, G.400 Chain G: P.183, L.184, F.187, Q.188, Y.189, Y.190, G.191, L.192, F.193, R.194 Chain X: L.9, R.10, I.13 Ligands: PEE.14, PC1.23, PEE.43 14 PLIP interactions: 4 interactions with chain X, 3 interactions with chain C, 7 interactions with chain G Hydrophobic interactions: X:L.9, X:I.13, C:Y.311, C:Y.311, G:F.187, G:F.193, G:F.193, G:F.193 Salt bridges: X:R.10, X:R.10, G:R.194 Hydrogen bonds: C:N.328, G:G.191, G:L.192 CDL.16: 29 residues within 4Å: Chain D: T.262, L.266, L.268, P.269, F.270, Y.272, F.273 Chain E: E.29, R.33, V.79, R.88, Q.91, T.94, L.95, I.98 Chain I: I.38, V.39, G.40, I.42, N.43, W.52, V.76, V.80 Chain S: F.69, I.70, N.71, F.74 Ligands: CDL.20, CDL.40 20 PLIP interactions: 2 interactions with chain I, 7 interactions with chain D, 6 interactions with chain E, 5 interactions with chain S Hydrogen bonds: I:G.40, I:N.43, E:E.29, E:R.33, S:I.70, S:N.71, S:N.71 Hydrophobic interactions: D:T.262, D:L.266, D:F.270, D:Y.272, D:Y.272, D:F.273, D:F.273, E:L.95, E:I.98, S:F.74, S:F.74 Salt bridges: E:R.88, E:R.88 CDL.20: 18 residues within 4Å: Chain E: G.25, V.26, L.27, E.29, Y.30, R.33 Chain I: G.40, K.41, I.42, N.43 Chain S: F.74, M.75, F.79, V.83, L.84, F.88 Ligands: CDL.16, CDL.40 9 PLIP interactions: 3 interactions with chain S, 4 interactions with chain E, 2 interactions with chain I Hydrophobic interactions: S:F.74, S:F.79, S:V.83, E:V.26, E:L.27, E:E.29 Hydrogen bonds: E:V.26, I:K.41, I:I.42 CDL.21: 28 residues within 4Å: Chain C: I.30, E.236, L.239, I.240, I.243, V.244 Chain G: L.129 Chain H: F.74, M.75, F.79, Y.82, V.83, L.84, R.86, F.87, F.88, W.92 Chain O: L.265, L.268, Y.272, K.276 Chain P: L.27, Y.30, N.31 Ligands: CDL.7, PC1.10, PC1.11, CDL.22 16 PLIP interactions: 5 interactions with chain O, 6 interactions with chain H, 3 interactions with chain C, 2 interactions with chain P Hydrophobic interactions: O:L.268, H:F.79, H:F.88, H:W.92, H:W.92, C:I.240, C:I.243, C:I.243, P:L.27, P:L.27 Hydrogen bonds: O:Y.272, O:Y.272, O:K.276, H:Y.82 Salt bridges: O:K.276, H:R.86 CDL.22: 29 residues within 4Å: Chain H: F.69, I.70, N.71, F.74 Chain O: L.266, P.269, F.270, F.273 Chain P: L.27, E.29, R.33, V.79, R.88, Q.91, T.94, L.95, I.98 Chain T: I.38, V.39, G.40, I.42, N.43, W.52, F.69, G.72, T.73, F.75, V.76 Ligands: CDL.21 15 PLIP interactions: 4 interactions with chain T, 7 interactions with chain P, 2 interactions with chain O, 2 interactions with chain H Hydrophobic interactions: T:W.52, T:V.76, P:L.27, P:T.94, P:L.95, P:I.98, O:L.266, O:F.273 Hydrogen bonds: T:G.40, T:N.43, P:R.33, H:I.70, H:N.71 Salt bridges: P:R.88, P:R.88 CDL.24: 38 residues within 4Å: Chain C: I.13, I.16, V.17, F.20, S.21, V.47, L.197, W.222, F.223 Chain L: R.495, R.499, W.504, Y.505, T.508 Chain N: M.1, W.3 Chain P: L.104, A.107, R.108, Y.110, A.111, V.114, I.115 Chain R: I.181, P.183, M.186, F.187 Chain T: P.63, Q.67 Chain V: Y.24, L.27, L.28, W.31 Ligands: CDL.6, PC1.9, PC1.11, UQ8.13, PC1.30 16 PLIP interactions: 1 interactions with chain T, 2 interactions with chain V, 2 interactions with chain R, 4 interactions with chain L, 1 interactions with chain N, 2 interactions with chain P, 4 interactions with chain C Hydrogen bonds: T:Q.67, L:T.508 Hydrophobic interactions: V:L.28, V:W.31, R:I.181, R:F.187, N:W.3, P:L.104, P:V.114, C:F.20, C:F.20, C:L.197, C:L.197 Salt bridges: L:R.495, L:R.499, L:R.499 CDL.27: 38 residues within 4Å: Chain A: R.495, R.499, W.504, Y.505, G.506, T.508 Chain C: M.1, W.3 Chain E: L.104, A.107, R.108, A.111 Chain G: I.181, P.183, M.186 Chain I: P.63, Q.67 Chain K: Y.24, L.27, L.28, W.31, S.32, T.35 Chain N: I.13, I.16, V.17, F.20, S.21, W.222, F.223 Ligands: PC1.1, PEE.14, PC1.19, PC1.23, PC1.28, PC1.29, CDL.31, UQ8.32 21 PLIP interactions: 3 interactions with chain N, 6 interactions with chain K, 5 interactions with chain A, 2 interactions with chain C, 2 interactions with chain E, 1 interactions with chain G, 2 interactions with chain I Hydrophobic interactions: N:V.17, N:F.20, N:F.223, K:L.27, K:L.28, K:W.31, K:W.31, K:W.31, C:M.1, C:W.3, E:L.104, E:A.111, G:I.181, I:Q.67 Hydrogen bonds: K:Y.24, A:G.506, A:T.508, I:Q.67 Salt bridges: A:R.495, A:R.499, A:R.499 CDL.31: 31 residues within 4Å: Chain C: T.7, T.11, F.121, L.125, W.166, V.187, L.188, F.190, F.191, Y.194, L.195, I.198 Chain G: K.180, I.181, T.182, P.183 Chain N: T.11, S.12, I.13, I.16, L.46, F.190, A.193, Y.194, L.197 Ligands: PC1.1, CDL.6, UQ8.12, PC1.19, CDL.27, UQ8.32 19 PLIP interactions: 12 interactions with chain C, 4 interactions with chain N, 3 interactions with chain G Hydrophobic interactions: C:L.125, C:V.187, C:F.191, C:F.191, C:F.191, C:F.191, C:F.191, C:Y.194, C:Y.194, C:Y.194, N:I.13, N:Y.194 Hydrogen bonds: C:T.11, C:Y.194, N:T.11, N:I.13, G:I.181, G:T.182 Salt bridges: G:K.180 CDL.33: 38 residues within 4Å: Chain N: D.29, I.30, N.31, F.34, R.86, D.89, M.90, I.93, F.97, F.100, R.101, Y.104, E.210, I.237, I.240, V.241, V.244, C.245, Y.249, W.280, E.350, F.359, W.360, L.363, L.367 Chain R: R.130 Chain S: W.92, R.95, N.96, I.97, F.100, V.104, L.105, Y.108 Ligands: PC1.29, PC1.34, CDL.40, CDL.41 25 PLIP interactions: 14 interactions with chain N, 10 interactions with chain S, 1 interactions with chain R Hydrophobic interactions: N:D.89, N:F.97, N:F.100, N:I.237, N:I.240, N:V.241, N:V.241, N:F.359, N:L.367, S:W.92, S:W.92, S:N.96, S:F.100, S:V.104, S:Y.108, S:Y.108, S:Y.108 Hydrogen bonds: N:Y.104, N:E.210, N:E.350, S:N.96 Salt bridges: N:R.101, N:R.101, S:R.95, R:R.130 CDL.38: 29 residues within 4Å: Chain N: K.296, I.297, F.300, Y.304, F.307, I.308, Y.311, V.314, I.315, N.319, T.325, R.327, N.328, G.400 Chain R: Q.188, Y.189, Y.190, G.191, L.192, F.193, R.194 Chain V: L.18, V.22 Chain W: L.9, R.10, V.12, I.13, Y.16 Ligands: PC1.39 21 PLIP interactions: 5 interactions with chain R, 8 interactions with chain N, 7 interactions with chain W, 1 interactions with chain V Hydrophobic interactions: R:L.192, R:F.193, N:K.296, N:F.300, N:F.300, N:Y.311, N:Y.311, W:V.12, W:I.13, W:I.13, W:Y.16, W:Y.16, V:L.18 Hydrogen bonds: R:Y.189, R:G.191, N:N.319, N:N.328, N:N.328 Salt bridges: R:R.194, W:R.10, W:R.10 CDL.40: 26 residues within 4Å: Chain D: F.261, L.265, L.268, P.269, Y.272, K.276 Chain N: I.30, E.236, L.239, I.240, I.243 Chain S: F.74, M.75, F.79, Y.82, V.83, L.84, R.86, F.87, F.88, W.92 Ligands: CDL.16, CDL.20, PC1.29, CDL.33, CDL.41 13 PLIP interactions: 4 interactions with chain D, 7 interactions with chain S, 2 interactions with chain N Hydrophobic interactions: D:L.265, D:L.265, S:F.87, S:F.88, S:F.88, S:W.92, S:W.92, N:I.240, N:I.243 Hydrogen bonds: D:Y.272, D:Y.272, S:Y.82 Salt bridges: S:R.86 CDL.41: 17 residues within 4Å: Chain N: L.353, I.357 Chain R: K.65, F.66, W.70 Chain S: F.88, K.89, W.92, Y.93, I.97, R.98, W.101, F.102, L.105, I.106 Ligands: CDL.33, CDL.40 12 PLIP interactions: 7 interactions with chain S, 4 interactions with chain R, 1 interactions with chain N Hydrophobic interactions: S:Y.93, S:F.102, S:F.102, R:F.66, R:F.66, R:F.66, N:L.353 Hydrogen bonds: S:Y.93, S:W.101 Salt bridges: S:K.89, S:R.98, R:K.65

3 x UQ8: Ubiquinone-8(Non-covalent)

UQ8.12: 33 residues within 4Å: Chain C: T.50, F.54, V.128, A.149, L.152, Y.153, F.156, W.166, I.167, F.168, R.180, L.181, Y.183, L.184, Y.186, V.187, L.188, F.190 Chain N: T.50, F.54, W.166, I.167, R.180, Y.183, L.184, Y.186, V.187, F.190 Ligands: HEM.3, CDL.6, HEM.25, CDL.31, UQ8.32 15 PLIP interactions: 5 interactions with chain N, 10 interactions with chain C Hydrophobic interactions: N:F.54, N:Y.183, N:Y.186, N:V.187, N:F.190, C:T.50, C:V.128, C:L.152, C:W.166, C:I.167, C:L.184, C:L.184, C:L.184, C:V.187, C:F.190 UQ8.13: 18 residues within 4Å: Chain C: Y.19, F.20, M.23, F.36, F.39, L.40, L.197, G.200, V.201, M.203, H.204, W.222, E.230 Chain V: L.28 Ligands: HEM.4, CDL.6, PC1.9, CDL.24 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain V Hydrophobic interactions: C:F.20, C:F.20, C:F.36, C:F.39, C:F.39, C:F.39, C:L.40, C:W.222, V:L.28 Hydrogen bonds: C:W.222 UQ8.32: 30 residues within 4Å: Chain C: W.166 Chain E: V.114, L.118 Chain N: Y.19, F.20, M.23, V.25, F.36, F.39, L.40, A.43, V.47, T.50, M.51, F.54, F.190, L.197, G.200, V.201, M.203, H.204, W.207, W.222, L.227, E.230 Ligands: UQ8.12, PC1.19, HEM.26, CDL.27, CDL.31 10 PLIP interactions: 9 interactions with chain N, 1 interactions with chain E Hydrophobic interactions: N:F.20, N:F.20, N:F.36, N:F.36, N:F.39, N:V.47, N:F.190, N:W.222, N:L.227, E:L.118

2 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.14: 23 residues within 4Å: Chain C: F.156, F.157, W.288, C.292, F.294, H.295, K.296, I.297, F.300, G.301, Y.304, M.393, F.396 Chain X: V.12, I.13, Y.16, P.17, Y.19, V.20, L.23 Ligands: CDL.8, PC1.19, CDL.27 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain X Hydrophobic interactions: C:W.288, C:I.297, C:F.300, C:F.300, C:F.300, C:Y.304, C:Y.304, C:F.396, C:F.396, X:I.13, X:Y.16, X:Y.16, X:V.20 Hydrogen bonds: C:K.296, X:Y.16 Salt bridges: C:K.296 PEE.43: 20 residues within 4Å: Chain G: I.7, W.9, E.10, N.14, R.20, Q.21, R.22, L.192, F.193, W.198, D.199, F.201, Y.208 Chain K: L.18 Chain X: P.3, V.4, F.5, L.6 Ligands: CDL.8, PC1.23 8 PLIP interactions: 3 interactions with chain G, 1 interactions with chain K, 4 interactions with chain X Hydrogen bonds: G:N.14, G:D.199, X:V.4, X:F.5 Salt bridges: G:R.20 Hydrophobic interactions: K:L.18, X:F.5, X:L.6

2 x HEC: HEME C(Covalent)

HEC.15: 28 residues within 4Å: Chain D: V.76, F.77, N.80, C.81, N.83, C.84, H.85, N.154, V.157, W.158, P.159, T.160, F.162, I.165, R.168, Y.174, I.175, I.178, S.179, K.196, F.202, I.207, G.208, M.209, P.210, Q.212, L.213, V.235 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:N.154, D:V.157, D:V.157, D:P.159, D:F.162, D:Y.174, D:I.175, D:I.175, D:F.202, D:I.207, D:V.235, D:V.235 Hydrogen bonds: D:T.160, D:T.160, D:Y.174, D:G.208 Salt bridges: D:R.168, D:K.196 Metal complexes: D:H.85 HEC.36: 27 residues within 4Å: Chain O: V.76, N.80, C.81, N.83, C.84, H.85, N.154, V.157, W.158, P.159, T.160, F.162, I.165, R.168, Y.174, I.175, I.178, S.179, K.196, F.202, I.207, G.208, M.209, P.210, Q.212, L.213, V.235 20 PLIP interactions: 20 interactions with chain O, Hydrophobic interactions: O:N.154, O:V.157, O:V.157, O:P.159, O:Y.174, O:I.175, O:F.202, O:I.207, O:Q.212, O:L.213, O:V.235 Hydrogen bonds: O:T.160, O:Y.174, O:Y.174, O:G.208 Salt bridges: O:R.168, O:K.196 pi-Stacking: O:H.85, O:F.162 Metal complexes: O:H.85

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.17: 8 residues within 4Å: Chain E: C.197, H.199, L.200, C.202, C.216, C.218, H.219, S.221 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.197, E:H.199, E:C.216, E:H.219 FES.37: 8 residues within 4Å: Chain P: C.197, H.199, L.200, C.202, C.216, C.218, H.219, S.221 6 PLIP interactions: 6 interactions with chain P, Metal complexes: P:H.199, P:C.202, P:C.216, P:C.218, P:C.218, P:H.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muhleip, A. et al., Structural basis of mitochondrial membrane bending by the I-II-III 2 -IV 2 supercomplex. Nature (2023)

Release Date

2023-03-29

Peptides

Peptidase M16 inactive domain protein: AL
M16 family peptidase, putative: BM
Apocytochrome b: CN
Cytochrome protein c1: DO
Rieske iron-sulfur protein, ubiquinol-cytochrome C reductase iron-sulfur subunit: EP
Ubiquinol-cytochrome C reductase hinge protein: FQ
UQCRTT1: GR
Transmembrane protein, putative: HS
Transmembrane protein, putative: IT
UQCRTT3/UP1: JU
Transmembrane protein, putative: KV
UQCRTT2: WX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L
a

B
B

M
b

C
C

N
c

D
D

O
d

E
E

P
e

F
F

Q
f

G
G

R
g

H
H

S
h

I
I

T
i

J
J

U
j

K
K

V
k

W
l

X
L

Membrane

We predict this structure to be a membrane protein.
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Peptidase M16 inactive domain protein

M16 family peptidase, putative

Apocytochrome b

Cytochrome protein c1

Rieske iron-sulfur protein, ubiquinol-cytochrome C reductase iron-sulfur subunit

Ubiquinol-cytochrome C reductase hinge protein

UQCRTT1

Transmembrane protein, putative

Transmembrane protein, putative

UQCRTT3/UP1

Transmembrane protein, putative

UQCRTT2

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