SMTL ID : 8bel.1

Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CIII membrane domain)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

HEM.1: 23 residues within 4Å: Chain A: W.36, G.39, S.40, A.42, G.43, F.95, V.99, H.102, I.103, R.105, S.111, V.119, W.120, G.123, V.124, I.126, F.127, S.200, H.203, L.207, S.212, N.213 Ligands: UQ5.3 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:A.42, A:F.95, A:V.99, A:I.103, A:I.103, A:V.119, A:W.120, A:W.120, A:V.124, A:I.126, A:F.127, A:L.207 Hydrogen bonds: A:G.39, A:S.111, A:N.213 Water bridges: A:W.36, A:G.37, A:H.102, A:H.102 Salt bridges: A:H.102, A:R.105, A:R.105 Metal complexes: A:H.102, A:H.203 HEM.2: 24 residues within 4Å: Chain A: L.46, Q.49, I.50, G.53, V.54, L.56, A.57, Y.60, R.85, H.88, A.89, A.92, F.95, T.133, A.134, G.137, Y.138, L.140, P.141, H.189, Y.190, P.193, F.194, Y.280 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:L.46, A:Q.49, A:Y.60, A:A.89, A:A.92, A:F.95, A:T.133, A:L.140, A:L.140, A:Y.190, A:P.193, A:F.194 Water bridges: A:R.85, A:R.85, A:N.262 Salt bridges: A:R.85, A:R.85 pi-Stacking: A:H.88, A:H.189, A:H.189 Metal complexes: A:H.88, A:H.189 HEM.13: 20 residues within 4Å: Chain C: V.102, C.103, C.106, H.107, N.171, A.174, P.176, P.177, L.179, V.182, R.186, Y.192, L.196, L.197, F.219, I.224, A.225, M.226, M.229, L.230 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:V.102, C:N.171, C:A.174, C:P.176, C:P.177, C:L.179, C:L.179, C:V.182, C:L.196, C:L.197, C:L.197, C:F.219, C:I.224, C:L.230 Hydrogen bonds: C:A.225 Water bridges: C:R.186 Salt bridges: C:R.186 Metal complexes: C:H.107 HEM.20: 22 residues within 4Å: Chain H: W.36, G.39, S.40, A.42, G.43, F.95, V.99, H.102, I.103, R.105, S.111, W.120, G.123, V.124, I.126, F.127, S.200, H.203, L.207, S.212, N.213 Ligands: UQ5.22 25 PLIP interactions: 25 interactions with chain H, Hydrophobic interactions: H:A.42, H:F.95, H:V.99, H:I.103, H:I.103, H:W.120, H:W.120, H:V.124, H:I.126, H:F.127, H:L.207 Hydrogen bonds: H:G.39, H:S.111, H:S.212, H:N.213 Water bridges: H:W.36, H:G.37, H:F.38, H:N.213, H:N.213 Salt bridges: H:H.102, H:R.105, H:R.105 Metal complexes: H:H.102, H:H.203 HEM.21: 25 residues within 4Å: Chain H: L.46, Q.49, I.50, G.53, V.54, A.57, Y.60, V.71, R.85, H.88, A.89, A.92, M.130, T.133, A.134, G.137, Y.138, L.140, P.141, F.186, H.189, Y.190, P.193, F.194, Y.280 21 PLIP interactions: 21 interactions with chain H, Hydrophobic interactions: H:L.46, H:Q.49, H:Y.60, H:V.71, H:A.92, H:T.133, H:A.134, H:L.140, H:L.140, H:F.186, H:Y.190, H:Y.190, H:P.193, H:F.194 Water bridges: H:N.262, H:N.262 Salt bridges: H:R.85, H:R.85 pi-Stacking: H:H.189 Metal complexes: H:H.88, H:H.189 HEM.34: 19 residues within 4Å: Chain J: V.102, C.103, C.106, H.107, N.171, Y.175, P.176, P.177, V.182, R.186, Y.192, L.196, L.197, F.219, I.224, A.225, M.226, M.229, L.230 17 PLIP interactions: 17 interactions with chain J, Hydrophobic interactions: J:V.102, J:P.176, J:P.176, J:P.177, J:V.182, J:L.196, J:L.197, J:F.219, J:I.224, J:A.225, J:M.226, J:L.230 Hydrogen bonds: J:Y.192, J:A.225 Salt bridges: J:R.186 pi-Cation interactions: J:H.107 Metal complexes: J:H.107

3 x UQ5: 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE(Non-covalent)

UQ5.3: 14 residues within 4Å: Chain A: H.22, L.23, Y.26, S.40, G.43, V.47, V.197, S.200, L.201, L.204, H.208, F.227 Ligands: HEM.1, PGT.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.197, A:L.201, A:F.227, A:F.227 UQ5.4: 19 residues within 4Å: Chain A: I.131, V.132, F.135, G.149, V.152, I.153, W.170, L.171, F.185, L.188, I.275, V.276, P.277, F.281, I.284, Y.285 Chain H: F.55 Chain I: M.138, H.237 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain H Hydrophobic interactions: A:I.131, A:V.132, A:I.153, A:I.153, A:I.153, A:W.170, A:L.171, A:F.185, A:L.188, A:P.277, A:F.281, A:F.281, A:I.284, A:Y.285, H:F.55 UQ5.22: 17 residues within 4Å: Chain H: H.22, L.23, Y.26, T.28, S.40, G.43, L.46, V.47, V.197, S.200, L.201, L.204, H.208, S.212, F.227 Ligands: HEM.20, PGT.25 11 PLIP interactions: 11 interactions with chain H Hydrophobic interactions: H:L.23, H:L.46, H:V.47, H:V.197, H:V.197, H:L.201, H:F.227, H:F.227 Hydrogen bonds: H:S.212 Water bridges: H:S.40 pi-Stacking: H:F.227

6 x 3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE(Non-covalent)

3PH.5: 9 residues within 4Å: Chain A: I.97, F.245, W.249, V.256, L.257, W.279 Ligands: PGT.7, CDL.9, PC7.10 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.97, A:F.245, A:W.249, A:L.257, A:W.279, A:W.279, A:W.279 3PH.14: 7 residues within 4Å: Chain D: I.34, H.35, V.38, W.42, T.46 Ligands: CDL.9, CDL.16 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.34, D:V.38, D:W.42, D:W.42 Salt bridges: D:H.35 3PH.18: 6 residues within 4Å: Chain C: I.83, S.85 Chain F: L.49, N.53 Ligands: PGT.7, CDL.16 7 PLIP interactions: 2 interactions with chain F, 5 interactions with chain C Hydrophobic interactions: F:L.49, C:I.83 Hydrogen bonds: F:N.53 Water bridges: C:I.83, C:L.84, C:S.85, C:S.85 3PH.24: 14 residues within 4Å: Chain H: A.241, I.244, F.245, I.248, W.249, Y.252, A.253 Chain J: G.82, I.83, F.272, I.275, F.276, S.279 Ligands: CDL.35 14 PLIP interactions: 8 interactions with chain H, 6 interactions with chain J Hydrophobic interactions: H:I.244, H:F.245, H:I.248, H:I.248, H:W.249, H:W.249, H:Y.252, H:A.253, J:I.83, J:F.272, J:F.272, J:F.276, J:F.276 Hydrogen bonds: J:G.82 3PH.37: 7 residues within 4Å: Chain A: V.162, V.163, T.166 Chain N: I.35, P.40, W.43 Ligands: 3PH.38 2 PLIP interactions: 1 interactions with chain N, 1 interactions with chain A Hydrophobic interactions: N:I.35, A:T.166 3PH.38: 10 residues within 4Å: Chain A: W.170, V.298 Chain I: V.131, L.132, I.135, V.136 Chain N: V.37, V.38 Ligands: CDL.32, 3PH.37 10 PLIP interactions: 2 interactions with chain N, 6 interactions with chain A, 2 interactions with chain I Hydrophobic interactions: N:V.37, N:V.38, A:W.170, A:W.170, A:W.170, A:W.170, A:W.170, A:V.298, I:L.132, I:I.135

4 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PGT.6: 14 residues within 4Å: Chain A: S.9, L.10, L.11, V.24, S.40, G.43, I.44, V.47, Y.228, Y.232, W.239 Ligands: UQ5.3, CDL.8, PTY.19 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.10, A:I.44, A:V.47, A:Y.228, A:Y.228, A:Y.232, A:W.239, A:W.239 Hydrogen bonds: A:L.10 PGT.7: 18 residues within 4Å: Chain A: A.241, I.244, F.245, I.248, W.249, Y.252, A.253, V.256 Chain C: G.82, I.83, K.268, F.272, I.275, F.276, S.279 Ligands: 3PH.5, CDL.16, 3PH.18 16 PLIP interactions: 10 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:A.241, A:I.244, A:F.245, A:F.245, A:I.248, A:I.248, A:W.249, A:W.249, A:Y.252, C:I.83, C:F.272, C:I.275, C:F.276 Hydrogen bonds: A:Y.252, C:G.82, C:G.82 PGT.15: 18 residues within 4Å: Chain A: R.325, P.326, I.327, G.330, M.331, L.334, L.335, V.364, F.368, L.375, V.378, G.379, I.382, Y.386 Chain D: S.39, E.40, W.42, I.43 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:R.325, A:I.327, A:L.334, A:L.335, A:V.364, A:F.368, A:V.378, A:I.382, D:I.43 Water bridges: A:G.330, D:I.43 Hydrogen bonds: D:E.40 PGT.25: 14 residues within 4Å: Chain H: S.9, L.10, L.11, L.23, V.24, S.40, G.43, I.44, Y.228, Y.232, W.239 Ligands: UQ5.22, CDL.32, PTY.39 12 PLIP interactions: 12 interactions with chain H Hydrophobic interactions: H:L.10, H:L.11, H:L.23, H:V.24, H:I.44, H:Y.228, H:Y.232, H:W.239, H:W.239 Hydrogen bonds: H:S.9, H:L.10, H:L.11

7 x CDL: CARDIOLIPIN(Non-covalent)

CDL.8: 23 residues within 4Å: Chain A: I.44, I.48, V.51, M.87, Y.228, Y.232, L.236, W.239, V.240, A.243, S.247 Chain B: R.120, Y.123, A.124, L.127, L.129, L.130, L.134 Chain C: W.274, Y.288 Ligands: PGT.6, PC7.12, PTY.19 25 PLIP interactions: 10 interactions with chain A, 12 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: A:I.44, A:I.48, A:V.51, A:V.51, A:Y.232, A:L.236, A:W.239, A:V.240, A:A.243, B:Y.123, B:Y.123, B:Y.123, B:A.124, B:L.127, B:L.127, B:L.129, B:L.130, B:L.130, B:L.134, C:W.274 Hydrogen bonds: A:Y.232, C:Y.288, C:Y.288 Water bridges: B:R.120 Salt bridges: B:R.120 CDL.9: 26 residues within 4Å: Chain A: S.33, Y.34, W.35, F.38, L.41, L.101, Y.109, G.238, A.241, F.242, W.333, L.336, L.340 Chain D: K.37, V.38, N.41, A.45, T.46, L.48, V.49, V.52, V.53 Ligands: 3PH.5, PC7.10, 3PH.14, CDL.16 16 PLIP interactions: 7 interactions with chain D, 9 interactions with chain A Hydrophobic interactions: D:V.38, D:L.48, D:V.49, D:V.52, D:V.53, A:Y.34, A:W.35, A:F.38, A:L.41, A:W.333, A:L.336 Hydrogen bonds: D:N.41, A:Y.34, A:Y.109 Salt bridges: D:K.37 Water bridges: A:S.33 CDL.16: 19 residues within 4Å: Chain A: Y.34, I.244, I.248 Chain C: S.279, L.282, L.283, A.286, R.289, R.290 Chain D: L.26, W.27, L.30, K.33, I.34, K.37 Ligands: PGT.7, CDL.9, 3PH.14, 3PH.18 19 PLIP interactions: 3 interactions with chain A, 9 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: A:I.244, A:I.248, D:L.26, D:W.27, D:W.27, D:W.27, D:L.30, D:I.34, C:L.282, C:A.286 Water bridges: A:Y.34, C:R.289, C:R.289, C:R.290 Salt bridges: D:K.33, D:K.37, D:K.37, C:R.289, C:R.290 CDL.27: 19 residues within 4Å: Chain H: S.33, Y.34, W.35, F.38, L.41, L.101, G.238, A.241, F.242, F.245 Chain K: K.37, V.38, N.41, W.42, A.45, T.46, L.48 Ligands: PC7.28, CDL.35 18 PLIP interactions: 7 interactions with chain K, 11 interactions with chain H Hydrophobic interactions: K:V.38, K:N.41, K:W.42, K:A.45, K:L.48, H:Y.34, H:Y.34, H:F.38, H:F.38, H:L.41, H:L.101, H:L.101, H:F.245 Hydrogen bonds: K:N.41, H:Y.34 Salt bridges: K:K.37 Water bridges: H:K.234, H:K.234 CDL.32: 22 residues within 4Å: Chain H: I.48, V.51, M.87, Y.228, Y.232, L.236, W.239, F.246, S.247, F.251 Chain I: R.120, Y.123, A.124, L.127, L.130, L.134 Chain J: W.274, Y.288 Ligands: PGT.25, PC7.33, 3PH.38, PTY.39 22 PLIP interactions: 9 interactions with chain I, 9 interactions with chain H, 4 interactions with chain J Hydrophobic interactions: I:Y.123, I:Y.123, I:L.127, I:L.130, I:L.130, I:L.134, I:L.134, H:I.48, H:I.48, H:V.51, H:Y.232, H:L.236, H:W.239, H:F.246, H:F.251, J:W.274 Hydrogen bonds: I:R.120, H:Y.232, J:Y.288, J:Y.288 Salt bridges: I:R.120 Water bridges: J:Y.288 CDL.35: 20 residues within 4Å: Chain H: Y.34, A.241, I.244, F.245 Chain J: I.275, S.279, L.282, L.283, A.286, R.289, R.290 Chain K: L.26, W.27, P.31, K.33, I.34, K.37 Ligands: 3PH.24, CDL.27, CDL.36 17 PLIP interactions: 6 interactions with chain J, 5 interactions with chain K, 6 interactions with chain H Hydrophobic interactions: J:I.275, J:L.282, J:L.283, K:W.27, K:P.31, K:I.34, H:A.241, H:I.244, H:F.245, H:F.245 Water bridges: J:R.289, H:Y.34, H:K.234 Salt bridges: J:R.289, J:R.290, K:K.33, K:K.37 CDL.36: 21 residues within 4Å: Chain I: Y.101, F.111, V.115, G.118, G.119, F.121, V.122, S.125 Chain J: L.277, L.280, L.283, Q.284, Y.287 Chain K: K.21, I.22, M.23, T.24, W.27 Chain M: G.38, E.39 Ligands: CDL.35 15 PLIP interactions: 5 interactions with chain K, 3 interactions with chain I, 7 interactions with chain J Hydrophobic interactions: K:W.27, I:V.115, I:V.122, J:L.277, J:L.280, J:L.280, J:L.283, J:L.283, J:Q.284, J:Y.287 Hydrogen bonds: K:I.22, K:M.23, K:T.24, I:Y.101 Salt bridges: K:K.21

5 x PC7: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE(Non-covalent)

PC7.10: 15 residues within 4Å: Chain A: W.35, L.101, F.104, Y.108, Y.109, S.323, F.332, W.333, L.336 Chain D: N.41, S.44, A.45, L.48 Ligands: 3PH.5, CDL.9 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:W.35, A:W.35, A:L.101, A:Y.108, A:Y.108, A:Y.108, A:Y.109, A:W.333, A:W.333, A:L.336, A:L.336, D:L.48 Hydrogen bonds: A:Y.109, A:Y.109, A:S.323, D:S.44 Water bridges: A:S.33 Salt bridges: D:E.40 PC7.12: 11 residues within 4Å: Chain B: Y.113, R.120 Chain F: M.21, N.24, Y.27, V.28, I.31, I.32 Chain G: W.36 Ligands: CDL.8, PTY.19 8 PLIP interactions: 3 interactions with chain F, 4 interactions with chain B, 1 interactions with chain G Hydrophobic interactions: F:I.31, F:I.32, G:W.36 Hydrogen bonds: F:N.24 Water bridges: B:R.120 Salt bridges: B:R.120, B:R.120 pi-Cation interactions: B:Y.113 PC7.17: 21 residues within 4Å: Chain B: Y.101, F.111, F.114, V.115, S.117, G.118, F.121, V.122, S.125 Chain C: L.277, L.280, L.283, Q.284, Y.287 Chain D: K.21, I.22, M.23, T.24 Chain F: F.30, G.38, E.39 17 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F, 9 interactions with chain B, 4 interactions with chain C Hydrogen bonds: D:I.22, D:M.23, D:T.24, B:Y.101 Hydrophobic interactions: F:F.30, B:F.111, B:F.114, B:F.114, B:F.114, B:V.115, B:V.115, B:F.121, B:F.121, C:L.277, C:L.283, C:L.283, C:Q.284 PC7.28: 15 residues within 4Å: Chain H: W.35, Y.100, L.101, Y.108, Y.109, S.323, F.332, W.333, L.336 Chain K: E.40, N.41, S.44, A.45, V.49 Ligands: CDL.27 12 PLIP interactions: 9 interactions with chain H, 3 interactions with chain K Hydrophobic interactions: H:W.35, H:Y.100, H:L.101, H:Y.108, H:W.333, H:L.336, K:V.49 Hydrogen bonds: H:Y.109, H:Y.109, H:S.323, K:S.44 Salt bridges: K:E.40 PC7.33: 13 residues within 4Å: Chain I: Y.113, R.120 Chain M: M.21, N.24, Y.27, V.28, I.32 Chain N: A.30, G.33, A.34, W.36 Ligands: CDL.32, PTY.39 8 PLIP interactions: 5 interactions with chain I, 1 interactions with chain N, 2 interactions with chain M Hydrogen bonds: I:Y.113 Water bridges: I:R.109, I:R.109 Salt bridges: I:R.120, I:R.120 Hydrophobic interactions: N:W.36, M:V.28, M:I.32

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

FES.11: 10 residues within 4Å: Chain B: C.215, H.217, L.218, G.219, C.220, C.234, C.236, H.237, S.239, P.251 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.215, B:H.217, B:C.234, B:H.237 FES.31: 10 residues within 4Å: Chain I: C.215, H.217, L.218, G.219, C.220, C.234, C.236, H.237, S.239, P.251 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.215, I:H.217, I:C.234, I:H.237

3 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.19: 5 residues within 4Å: Chain F: N.24 Chain G: W.26 Ligands: PGT.6, CDL.8, PC7.12 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:W.26, G:W.26, G:W.26, G:W.26 PTY.26: 6 residues within 4Å: Chain H: P.326, M.331, L.334, V.364, F.368 Chain K: I.43 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:V.364, H:F.368 PTY.39: 5 residues within 4Å: Chain M: N.24 Chain N: W.26 Ligands: PGT.25, CDL.32, PC7.33 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:N.24

1 x UQ7: UBIQUINONE-7(Non-covalent)

UQ7.23: 24 residues within 4Å: Chain A: V.51, F.55, M.58 Chain B: V.131, L.134, I.135, M.138, H.237 Chain H: I.131, V.132, F.135, I.136, G.149, V.152, I.153, W.170, F.185, L.188, I.275, V.276, P.277, F.281, I.284, Y.285 20 PLIP interactions: 3 interactions with chain B, 16 interactions with chain H, 1 interactions with chain A Hydrophobic interactions: B:V.131, B:L.134, B:I.135, H:I.131, H:F.135, H:I.136, H:I.153, H:I.153, H:I.153, H:W.170, H:F.185, H:L.188, H:L.188, H:P.277, H:P.277, H:F.281, H:I.284, H:Y.285, H:Y.285, A:V.51

2 x Q7G: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside(Non-covalent)

Q7G.29: 7 residues within 4Å: Chain H: P.292, L.303, Q.359, S.362, L.363, F.366 Ligands: Q7G.30 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:P.292, H:L.303, H:Q.359, H:Q.359, H:F.366 Q7G.30: 5 residues within 4Å: Chain H: I.291, P.292, D.293, G.296 Ligands: Q7G.29 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:I.291, H:D.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klusch, N. et al., Cryo-EM structure of the respiratory I + III 2 supercomplex from Arabidopsis thaliana at 2 angstrom resolution. Nat.Plants (2023)

Release Date

2023-01-11

Peptides

Cytochrome b: AH
Cytochrome b-c1 complex subunit Rieske-1, mitochondrial: BI
Cytochrome c1 2, heme protein, mitochondrial: CJ
Cytochrome b-c1 complex subunit 8-1, mitochondrial: DK
Cytochrome b-c1 complex subunit 6-1, mitochondrial: EL
Cytochrome b-c1 complex subunit 9, mitochondrial: FM
Cytochrome b-c1 complex subunit 10, mitochondrial: GN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

H
M

B
D

I
N

C
E

J
O

D
G

K
Q

E
H

L
R

F
I

M
S

G
J

N
T

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b

Cytochrome b-c1 complex subunit Rieske-1, mitochondrial

Cytochrome c1 2, heme protein, mitochondrial

Cytochrome b-c1 complex subunit 8-1, mitochondrial

Cytochrome b-c1 complex subunit 6-1, mitochondrial

Cytochrome b-c1 complex subunit 9, mitochondrial

Cytochrome b-c1 complex subunit 10, mitochondrial

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