SMTL ID : 6rfr.1

Cryo-EM structure of respiratory complex I from Yarrowia lipolytica at 3.2 A resolution

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.20 Å

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

6 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 12 residues within 4Å: Chain A: H.129, P.130, D.132, C.133, C.136, Q.138, C.142, L.144, Q.145, R.182, V.235, G.236 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:D.132 Metal complexes: A:H.129, A:C.133, A:C.136, A:C.142 SF4.2: 11 residues within 4Å: Chain A: M.180, C.183, I.184, H.185, C.186, T.187, C.189, I.213, C.233, V.235, L.238 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.183, A:C.186, A:C.189, A:C.233 SF4.4: 12 residues within 4Å: Chain B: P.225, S.380, C.381, G.382, Q.383, C.384, C.387, T.425, I.426, C.427, L.429, G.430 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.381, B:C.384, B:C.387, B:C.427 SF4.11: 12 residues within 4Å: Chain I: H.118, C.140, P.141, I.145, C.169, I.170, Y.171, C.172, G.173, Y.174, C.175, E.186 5 PLIP interactions: 5 interactions with chain I, Salt bridges: I:E.186 Metal complexes: I:C.140, I:C.169, I:C.172, I:C.175 SF4.12: 11 residues within 4Å: Chain I: C.130, I.131, A.132, C.133, K.134, L.135, C.136, I.147, C.179, A.183, I.184 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.130, I:C.133, I:C.136, I:C.179 SF4.16: 9 residues within 4Å: Chain C: R.141, H.226 Chain K: A.84, C.85, C.86, G.121, S.149, C.150, C.180 5 PLIP interactions: 5 interactions with chain K, Metal complexes: K:C.85, K:C.86, K:C.150, K:C.180, K:C.180

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

FES.3: 9 residues within 4Å: Chain A: R.67, C.69, Y.70, G.78, N.79, C.80, R.81, C.83, C.97 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.69, A:C.80, A:C.83, A:C.97 FES.10: 9 residues within 4Å: Chain H: C.127, P.131, C.132, C.168, L.169, G.170, A.171, C.172, M.177 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.127, H:C.132, H:C.168, H:C.172

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.5: 19 residues within 4Å: Chain B: G.86, R.87, G.88, A.90, K.97, N.118, D.120, E.121, E.123, Y.206, G.209, E.210, E.211, V.244, T.245, N.246, T.249, A.428, L.429 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:E.210, B:E.210, B:A.428, B:L.429 Hydrogen bonds: B:G.88, B:N.118, B:D.120, B:G.122, B:E.211, B:N.246 Salt bridges: B:K.97

15 x 3PE: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)

3PE.6: 21 residues within 4Å: Chain 3: F.28, I.32 Chain 8: P.184, L.187, I.188, F.190, I.191, F.202, S.292, W.295, V.296, F.303, N.307, F.311, I.315, L.319 Chain C: R.269 Chain I: Y.77, F.78, L.80 Ligands: PLC.21 17 PLIP interactions: 13 interactions with chain 8, 1 interactions with chain I, 2 interactions with chain 3, 1 interactions with chain C Hydrophobic interactions: 8:P.184, 8:L.187, 8:L.187, 8:I.188, 8:F.190, 8:I.191, 8:F.202, 8:F.202, 8:W.295, 8:V.296, 8:F.311, 8:L.319, 8:L.319, I:L.80, 3:F.28, 3:I.32 Salt bridges: C:R.269 3PE.8: 12 residues within 4Å: Chain E: Y.133, E.134, T.135, K.136, Q.302, A.303, I.304, W.305, W.306, T.308 Chain K: W.207 Ligands: T7X.40 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:K.136, E:W.305 Hydrogen bonds: E:K.136, E:W.306, E:T.308 Salt bridges: E:K.136, E:K.136 3PE.13: 11 residues within 4Å: Chain J: D.93, G.94, W.95, A.127, G.130, W.134 Ligands: LMN.14, T7X.46 Chain b: S.173, I.216, V.220 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain b Hydrophobic interactions: J:A.127, b:I.216, b:V.220 Hydrogen bonds: J:G.94 3PE.15: 24 residues within 4Å: Chain 9: I.262, I.265, L.266 Chain J: V.35, G.38, A.39, A.43, A.46, R.47, F.139 Chain c: N.602, L.606, L.620, I.623, S.627, L.628, L.630, L.631, V.634, V.645, L.646, I.649, L.650, I.652 16 PLIP interactions: 9 interactions with chain c, 4 interactions with chain 9, 3 interactions with chain J Hydrophobic interactions: c:I.623, c:L.630, c:L.630, c:L.631, c:V.645, c:L.646, c:I.649, c:L.650, 9:I.262, 9:I.265, 9:L.266, 9:L.266, J:A.43, J:F.139 Hydrogen bonds: c:N.602 Salt bridges: J:R.47 3PE.24: 7 residues within 4Å: Chain T: F.28, R.29, V.32, A.36, L.37 Ligands: PLC.21, PLC.23 3 PLIP interactions: 3 interactions with chain T Hydrophobic interactions: T:A.36, T:L.37 Salt bridges: T:R.29 3PE.27: 18 residues within 4Å: Chain 9: Y.359, I.366, I.448, T.451 Chain R: R.117 Chain Y: F.19, K.23, P.28, A.29 Ligands: 3PE.41, 3PE.42, 3PE.45 Chain b: F.14, N.15, L.18, T.116, A.120, L.147 13 PLIP interactions: 4 interactions with chain b, 3 interactions with chain 9, 5 interactions with chain Y, 1 interactions with chain R Hydrophobic interactions: b:T.116, b:A.120, b:L.147, b:L.147, 9:I.366, 9:I.448, 9:T.451, Y:F.19, Y:F.19, Y:F.19 Hydrogen bonds: Y:A.29, R:R.117 Salt bridges: Y:K.23 3PE.29: 22 residues within 4Å: Chain 3: N.5, Y.15, L.16, S.19, R.23, L.26, F.27, A.29, F.30, A.31, G.33, I.34 Chain 8: P.318, F.321, G.322, L.325 Ligands: CDL.28 Chain a: I.99, V.103, I.106, N.107, N.109 15 PLIP interactions: 10 interactions with chain 3, 2 interactions with chain a, 3 interactions with chain 8 Hydrophobic interactions: 3:L.16, 3:L.26, 3:L.26, 3:F.27, 3:F.27, 3:A.29, 3:F.30, 3:A.31, a:V.103, 8:P.318, 8:F.321, 8:L.325 Hydrogen bonds: 3:N.5, a:N.107 Salt bridges: 3:R.23 3PE.35: 10 residues within 4Å: Chain 8: L.64, Y.70 Chain E: R.219, P.221, Y.351 Ligands: CDL.9 Chain a: F.16, L.19, I.23, Y.28 6 PLIP interactions: 2 interactions with chain 8, 3 interactions with chain a, 1 interactions with chain E Hydrophobic interactions: 8:Y.70, a:F.16, a:L.19, a:I.23, E:P.221 Hydrogen bonds: 8:L.64 3PE.36: 12 residues within 4Å: Chain 8: E.101, L.102, N.103 Chain D: I.42 Chain a: N.2, F.4, I.5 Chain d: A.44, M.45, Y.48, G.53, S.56 9 PLIP interactions: 4 interactions with chain a, 2 interactions with chain d, 3 interactions with chain 8 Hydrophobic interactions: a:F.4, a:F.4, a:I.5, d:Y.48, d:Y.48 Hydrogen bonds: a:N.2, 8:E.101, 8:N.103, 8:N.103 3PE.41: 14 residues within 4Å: Chain R: N.113 Chain Y: G.12, F.15, F.19, A.29, G.30, P.33, Y.36, V.37 Ligands: 3PE.27, 3PE.44 Chain b: L.11, N.15, R.16 9 PLIP interactions: 5 interactions with chain Y, 1 interactions with chain R, 3 interactions with chain b Hydrophobic interactions: Y:F.15, Y:F.19, Y:P.33, Y:Y.36, Y:Y.36, b:L.11 Hydrogen bonds: R:N.113, b:N.15 Salt bridges: b:R.16 3PE.42: 20 residues within 4Å: Chain 9: A.358, Y.359, L.362, A.365, F.369, P.376, L.377 Ligands: 3PE.27, 3PE.44, 3PE.45 Chain b: F.14, Y.28, N.110, S.111, N.112, L.113, T.116, A.143, P.146, I.150 18 PLIP interactions: 11 interactions with chain b, 7 interactions with chain 9 Hydrophobic interactions: b:F.14, b:T.116, b:A.143, b:P.146, b:P.146, b:I.150, b:I.150, 9:Y.359, 9:Y.359, 9:L.362, 9:A.365, 9:F.369, 9:L.377 Hydrogen bonds: b:Y.28, b:S.111, b:N.112, b:T.116, 9:Y.359 3PE.44: 17 residues within 4Å: Chain 9: P.376, L.377, F.452, F.454 Chain Y: T.5, G.9 Ligands: 3PE.41, 3PE.42, 3PE.45 Chain b: L.3, T.4, L.59, F.60, N.64, F.66, G.67, L.68 7 PLIP interactions: 4 interactions with chain 9, 3 interactions with chain b Hydrophobic interactions: 9:P.376, 9:L.377, 9:F.452, 9:F.452, b:L.59 Hydrogen bonds: b:N.64, b:L.68 3PE.45: 17 residues within 4Å: Chain 9: P.376 Ligands: 3PE.27, 3PE.42, 3PE.44 Chain b: F.38, F.55, N.56, F.57, L.59, L.68, L.123, V.124, L.126, L.127, W.130, L.140, A.143 13 PLIP interactions: 12 interactions with chain b, 1 interactions with chain 9 Hydrophobic interactions: b:F.38, b:F.38, b:F.57, b:L.59, b:L.123, b:L.123, b:V.124, b:L.126, b:W.130, b:W.130, b:L.140, b:A.143, 9:P.376 3PE.47: 18 residues within 4Å: Chain 5: S.14, M.15, T.16, G.18, W.19 Chain b: T.366, T.367, P.370, T.374, I.377, I.378, F.381 Chain c: W.16, L.20, F.21, H.112, R.115, L.152 16 PLIP interactions: 8 interactions with chain c, 6 interactions with chain b, 2 interactions with chain 5 Hydrophobic interactions: c:W.16, c:L.20, c:L.20, c:F.21, c:L.152, b:T.374, b:I.378, b:F.381 Salt bridges: c:H.112, c:R.115, c:R.115 Hydrogen bonds: b:T.367, b:T.367, b:T.374, 5:S.14, 5:G.18 3PE.49: 21 residues within 4Å: Chain X: S.81, P.82, D.83 Chain b: L.293, I.422, K.426 Chain c: Q.162, K.165, S.166, L.168, S.169, L.172, M.173, F.176, I.221, M.224, G.231, L.238, N.561, I.565, L.569 15 PLIP interactions: 9 interactions with chain c, 2 interactions with chain X, 4 interactions with chain b Hydrophobic interactions: c:L.168, c:L.172, c:F.176, c:I.221, c:I.565, c:I.565, c:L.569, b:L.293, b:I.422, b:I.422, b:K.426 Hydrogen bonds: c:Q.162, X:S.81, X:D.83 Salt bridges: c:K.165

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.7: 22 residues within 4Å: Chain E: G.60, N.62, G.63, F.64, L.65, R.85, L.109, L.128, I.129, G.130, R.131, F.138, V.143, S.167, A.168, F.169, F.179, K.183, P.202, A.203, M.205, K.211 18 PLIP interactions: 18 interactions with chain E Hydrophobic interactions: E:A.168, E:F.169, E:F.169 Hydrogen bonds: E:G.60, E:G.63, E:F.64, E:L.65, E:R.85, E:L.128, E:G.130, E:R.131, E:K.183, E:M.205 Salt bridges: E:R.85, E:R.131, E:K.211 pi-Cation interactions: E:R.85, E:R.85

6 x CDL: CARDIOLIPIN(Non-covalent)

CDL.9: 21 residues within 4Å: Chain 8: L.64, V.74 Chain E: D.215, R.216, R.219, S.220, P.221, C.222, V.224, L.289, L.293, Y.297, I.304, W.306 Ligands: 3PE.35, T7X.40 Chain a: F.16, A.20, I.23, L.24, Y.28 20 PLIP interactions: 5 interactions with chain a, 12 interactions with chain E, 3 interactions with chain 8 Hydrophobic interactions: a:F.16, a:A.20, a:I.23, a:L.24, a:Y.28, E:V.224, E:L.289, E:L.293, E:Y.297, E:Y.297, E:Y.297, E:W.306, E:W.306, 8:L.64, 8:V.74, 8:V.74 Hydrogen bonds: E:D.215, E:S.220 Salt bridges: E:R.216, E:R.219 CDL.25: 34 residues within 4Å: Chain 3: P.37, A.40, L.41 Chain 8: Y.332 Chain 9: M.1, I.3, L.4 Chain U: H.27, F.28, K.29, A.84, F.87, G.88, S.129, S.130, L.131, F.153, P.154, W.155, F.156, F.158, V.159, N.160 Ligands: CDL.28 Chain a: N.85, Y.86, F.88, T.89, I.90, L.92, L.93 Chain d: F.160, L.163, V.164 27 PLIP interactions: 12 interactions with chain U, 2 interactions with chain 8, 3 interactions with chain 3, 4 interactions with chain a, 4 interactions with chain d, 2 interactions with chain 9 Hydrophobic interactions: U:F.87, U:F.153, U:P.154, U:W.155, U:W.155, U:F.156, U:F.158, 8:Y.332, 3:A.40, 3:L.41, 3:L.41, a:Y.86, a:F.88, a:I.90, a:L.92, d:F.160, d:L.163, d:L.163, d:V.164, 9:I.3, 9:I.3 Hydrogen bonds: U:S.129, U:S.130, U:F.158, U:N.160, 8:Y.332 Salt bridges: U:K.29 CDL.26: 17 residues within 4Å: Chain 4: S.4, L.5 Chain 8: V.287 Chain D: A.2, I.3, L.8, Y.11, G.12 Chain I: L.91, E.92, F.95 Chain W: S.17, W.21, L.24, R.25, L.28 Ligands: PLC.21 9 PLIP interactions: 1 interactions with chain 8, 2 interactions with chain D, 3 interactions with chain I, 3 interactions with chain W Hydrophobic interactions: 8:V.287, D:Y.11, I:L.91, I:F.95, I:F.95, W:L.28, W:L.28 Hydrogen bonds: D:A.2, W:W.21 CDL.28: 21 residues within 4Å: Chain 3: N.5, G.7, F.8, W.9, Y.15, F.30, P.37 Chain 9: L.4, S.8, T.11, F.12, M.15 Chain U: K.73, V.77, M.80, L.81, F.83, F.87 Ligands: CDL.25, 3PE.29 Chain a: L.96 13 PLIP interactions: 7 interactions with chain U, 5 interactions with chain 3, 1 interactions with chain a Hydrophobic interactions: U:M.80, U:L.81, U:F.83, U:F.83, U:F.83, U:F.87, 3:F.30, 3:F.30, 3:P.37, a:L.96 Salt bridges: U:K.73 Hydrogen bonds: 3:N.5, 3:F.8 CDL.31: 22 residues within 4Å: Chain 6: Y.48 Chain 9: F.397, I.408 Chain J: P.116, A.117, G.120, W.121, L.124, C.125, A.128 Ligands: T7X.46 Chain c: R.586, L.587, G.591, I.592, R.594, L.595, K.598, I.647, L.650, Y.651, S.655 14 PLIP interactions: 7 interactions with chain c, 4 interactions with chain J, 2 interactions with chain 9, 1 interactions with chain 6 Hydrophobic interactions: c:L.587, c:I.592, c:K.598, c:I.647, c:I.647, c:L.650, J:W.121, J:L.124, J:L.124, J:A.128, 9:F.397, 9:I.408 Salt bridges: c:K.598 Hydrogen bonds: 6:Y.48 CDL.43: 35 residues within 4Å: Chain 5: M.15, I.36, L.40 Chain 7: Y.20, K.23, W.24, V.27, L.31 Chain R: Y.169, A.173, L.176, I.177, L.179, L.180, M.183 Ligands: PLC.32 Chain b: L.90, V.333, F.337, Q.371, T.374, Y.375, I.448, K.451, F.452, N.455, I.456, I.458, I.459, S.460, I.463, I.464, M.471 Chain c: L.17, F.21 32 PLIP interactions: 12 interactions with chain b, 3 interactions with chain c, 6 interactions with chain R, 9 interactions with chain 7, 2 interactions with chain 5 Hydrophobic interactions: b:L.90, b:L.90, b:V.333, b:T.374, b:Y.375, b:I.456, b:I.458, b:I.459, b:I.463, b:I.464, c:L.17, c:F.21, c:F.21, R:L.176, R:L.176, R:I.177, R:L.179, R:L.180, 7:Y.20, 7:W.24, 7:W.24, 7:W.24, 7:W.24, 7:W.24, 7:V.27, 7:L.31, 5:I.36, 5:L.40 Hydrogen bonds: b:N.455, R:Y.169 Salt bridges: b:K.451, 7:K.23

2 x LMN: Lauryl Maltose Neopentyl Glycol(Non-covalent)

LMN.14: 17 residues within 4Å: Chain 9: L.391, Y.396, S.399 Chain J: K.92, D.93, H.97, G.133, W.134, T.135, G.136, A.145, F.163 Ligands: 3PE.13 Chain b: L.180, V.184, I.209, G.213 13 PLIP interactions: 8 interactions with chain J, 3 interactions with chain 9, 2 interactions with chain b Hydrophobic interactions: J:W.134, J:W.134, J:T.135, J:F.163, 9:L.391, 9:Y.396, 9:Y.396, b:V.184, b:V.184 Hydrogen bonds: J:K.92, J:D.93, J:A.145, J:H.160 LMN.30: 10 residues within 4Å: Chain 6: Y.48, T.49, R.50, G.53, T.56 Chain J: V.115, I.119 Chain X: K.31, E.34, P.35 6 PLIP interactions: 4 interactions with chain 6, 2 interactions with chain J Hydrophobic interactions: 6:Y.48, 6:R.50, 6:T.56, J:V.115, J:I.119 Hydrogen bonds: 6:R.50

7 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)

PLC.17: 10 residues within 4Å: Chain 8: F.41, F.51, V.55 Chain K: A.66, V.67, W.70, Q.73, R.199 Ligands: PLC.34, T7X.40 3 PLIP interactions: 2 interactions with chain 8, 1 interactions with chain K Hydrophobic interactions: 8:F.51, 8:F.51, K:W.70 PLC.21: 15 residues within 4Å: Chain I: K.76, L.79, A.81, F.84, L.91 Chain T: R.26, G.27, F.28, R.29, P.30, Y.33 Ligands: 3PE.6, PLC.23, 3PE.24, CDL.26 6 PLIP interactions: 5 interactions with chain I, 1 interactions with chain T Hydrophobic interactions: I:L.79, I:A.81, I:F.84, I:L.91, T:Y.33 Salt bridges: I:K.76 PLC.22: 8 residues within 4Å: Chain 8: I.326, T.330, F.334 Chain T: G.42, F.45, Y.46, L.49, Q.53 8 PLIP interactions: 3 interactions with chain 8, 1 interactions with chain 3, 4 interactions with chain T Hydrophobic interactions: 8:I.326, 8:F.334, 8:F.334, T:F.45, T:F.45, T:F.45, T:Y.46 pi-Cation interactions: 3:Y.52 PLC.23: 9 residues within 4Å: Chain I: Y.88 Chain T: R.26, G.27, F.28, R.29, Y.33 Chain W: L.28 Ligands: PLC.21, 3PE.24 6 PLIP interactions: 4 interactions with chain T, 2 interactions with chain I Hydrophobic interactions: T:Y.33, I:Y.88, I:Y.88 Hydrogen bonds: T:G.27 Salt bridges: T:R.26, T:R.26 PLC.32: 10 residues within 4Å: Chain 5: V.44, T.48, Y.51 Chain 7: Y.35 Ligands: CDL.43 Chain b: I.463, I.466 Chain c: C.13, L.64, F.65 5 PLIP interactions: 2 interactions with chain b, 1 interactions with chain c, 2 interactions with chain 5 Hydrophobic interactions: b:I.463, b:I.466, c:F.65, 5:V.44 Hydrogen bonds: 5:Y.51 PLC.34: 13 residues within 4Å: Chain 4: L.24, N.25, S.26, I.27 Chain 8: Y.21, N.40, F.41, V.42, G.43, Y.44, L.48 Chain K: W.70 Ligands: PLC.17 4 PLIP interactions: 3 interactions with chain 8, 1 interactions with chain K Hydrophobic interactions: 8:Y.44, 8:L.48, 8:L.48 Hydrogen bonds: K:W.70 PLC.48: 8 residues within 4Å: Chain Q: W.29 Chain c: I.296, C.297, K.431, F.536, N.537, I.543, Y.547 7 PLIP interactions: 7 interactions with chain c Hydrophobic interactions: c:I.296, c:F.536 Hydrogen bonds: c:N.299, c:Y.547 Salt bridges: c:K.431, c:K.431 pi-Cation interactions: c:Y.547

1 x ZN: ZINC ION(Non-covalent)

ZN.18: 4 residues within 4Å: Chain M: C.97, H.110, C.125, C.128 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.97, M:H.110, M:C.125, M:C.128

2 x ZMP: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate(Covalent)

ZMP.19: 18 residues within 4Å: Chain N: S.66, L.67 Chain O: Q.22, T.25, F.32, K.55, I.56, E.59, F.60, H.63, R.64, Q.72, L.75, G.79, E.82, F.96, Y.99, F.100 15 PLIP interactions: 15 interactions with chain O Hydrophobic interactions: O:Q.22, O:F.32, O:F.32, O:K.55, O:I.56, O:E.59, O:F.60, O:Q.72, O:L.75, O:F.96, O:F.96, O:Y.99, O:F.100 Hydrogen bonds: O:H.63 Salt bridges: O:R.64 ZMP.20: 19 residues within 4Å: Chain P: D.88, S.89, L.90 Chain Q: F.7, N.11, K.12, V.15, S.22, A.26, I.43, K.46, F.47, N.50, A.51, I.53, L.59, T.66, H.69, F.73 12 PLIP interactions: 10 interactions with chain Q, 2 interactions with chain P Hydrophobic interactions: Q:V.15, Q:V.15, Q:A.26, Q:K.46, Q:F.47, Q:A.51, Q:L.59, Q:F.73, P:L.90 Hydrogen bonds: Q:A.51, Q:A.51, P:S.89

1 x UQ9: Ubiquinone-9(Non-covalent)

UQ9.33: 14 residues within 4Å: Chain 8: L.16, F.17, A.20, R.27, A.50, F.51, D.53, A.54, L.57, V.225, F.228, R.297 Chain K: I.106, R.108 11 PLIP interactions: 10 interactions with chain 8, 1 interactions with chain K Hydrophobic interactions: 8:L.16, 8:F.17, 8:A.20, 8:F.51, 8:D.53, 8:A.54, 8:L.57, 8:V.225, 8:F.228, K:I.106 pi-Cation interactions: 8:R.297

4 x T7X: Phosphatidylinositol(Non-covalent)

T7X.37: 17 residues within 4Å: Chain 9: F.74, S.437, V.438, Y.441, S.445 Chain U: W.59, L.60 Chain Y: K.18, R.25, Y.32, G.35, F.38, S.39, A.42, W.43, L.46 Ligands: CPL.38 11 PLIP interactions: 1 interactions with chain U, 3 interactions with chain 9, 7 interactions with chain Y Hydrogen bonds: U:W.59, 9:S.437, Y:R.25, Y:R.25, Y:S.39 Hydrophobic interactions: 9:F.74, 9:V.438, Y:A.42, Y:W.43, Y:W.43 Salt bridges: Y:K.18 T7X.39: 25 residues within 4Å: Chain 9: I.166, L.167, Y.170, N.198, L.199, I.202, A.203, L.206, N.256, S.257, L.258, V.259 Chain L: L.8, V.9, F.12 Chain c: I.625, L.629, V.632, L.633, N.636 Chain d: L.104, I.106, S.107, L.118, K.121 25 PLIP interactions: 11 interactions with chain 9, 4 interactions with chain d, 6 interactions with chain c, 4 interactions with chain L Hydrophobic interactions: 9:I.166, 9:L.167, 9:Y.170, 9:L.199, 9:I.202, 9:A.203, 9:L.206, d:L.104, d:I.106, d:L.118, c:I.625, c:L.629, c:L.629, c:V.632, c:L.633, L:L.8, L:V.9, L:F.12, L:F.12 Hydrogen bonds: 9:N.256, 9:N.256, 9:L.258, 9:V.259, c:N.636 Salt bridges: d:K.121 T7X.40: 17 residues within 4Å: Chain 8: V.55, L.59 Chain E: W.305, W.306 Chain K: L.64, I.203, T.204, W.207 Ligands: 3PE.8, CDL.9, PLC.17 Chain a: I.23, L.24, L.25, A.26, V.27, Y.28 8 PLIP interactions: 4 interactions with chain K, 2 interactions with chain a, 2 interactions with chain 8 Hydrophobic interactions: K:L.64, K:L.64, K:I.203, K:T.204, a:L.25, 8:V.55, 8:L.59 Hydrogen bonds: a:L.24 T7X.46: 22 residues within 4Å: Chain 9: I.400, V.404, L.407, I.408, L.411 Chain C: A.36, L.37, G.38 Ligands: 3PE.13, CDL.31 Chain b: F.165, Y.166, M.169, F.170, S.173, F.177 Chain c: L.587, G.588, P.589, I.592, N.593, L.596 7 PLIP interactions: 4 interactions with chain 9, 3 interactions with chain b Hydrophobic interactions: 9:I.400, 9:V.404, 9:L.407, 9:I.408, b:F.170, b:F.177 Hydrogen bonds: b:Y.166

1 x CPL: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

CPL.38: 20 residues within 4Å: Chain 9: S.40, Y.43, S.63, Y.67, M.70, L.310, Y.311, T.314, L.378, L.449, G.453, Y.456, I.460, I.463, F.464, Y.467 Chain Y: V.49, L.50, V.53 Ligands: T7X.37 9 PLIP interactions: 2 interactions with chain Y, 7 interactions with chain 9 Hydrophobic interactions: Y:V.49, Y:L.50, 9:Y.311, 9:Y.311, 9:T.314, 9:L.378, 9:Y.456, 9:Y.456 Hydrogen bonds: 9:S.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parey, K. et al., High-resolution cryo-EM structures of respiratory complex I: Mechanism, assembly, and disease. Sci Adv (2019)

Release Date

2019-12-11

Peptides

Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I): A
Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I): B
Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I): C
Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I): D
Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I): E
Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I): F
Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I): G
Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I): H
Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I): I
Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I): J
Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I): K
Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I): L
Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I): M
Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I): N
Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I): O
Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I): P
Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I): Q
Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I): R
Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I): S
Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I): T
Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I): U
Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I): V
Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I): W
Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I): X
Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I): Y
Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I): Z
Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I): 0
Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I): 1
Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I): 2
Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I): 3
Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I): 4
Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I): 5
Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I): 6
Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I): 7
Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I): 8
Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I): 9
Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I): a
Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I): b
Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I): c
Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I): d
Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I): e
Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I): f

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
O

O
P

P
Q

Q
R

R
S

S
U

T
W

U
X

V
Y

W
Z

X
a

Y
b

Z
c

0
d

1
e

2
f

3
g

4
h

5
i

6
j

7
n

8
1

9
2

a
3

b
4

c
5

d
6

e
8

f
9

Membrane

We predict this structure to be a membrane protein.
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Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)

Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)

Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)

Related Entries With Identical Sequence