SMTL ID : 8zee.1

Cryo-EM structure of an intermediate-state PSII-PRF2' complex during the process of photosystem II repair

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

35 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.1: 7 residues within 4Å: Chain A: W.185, G.186, A.187, F.190 Chain E: I.67 Ligands: CLA.2, BCR.37 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E, Hydrophobic interactions: A:A.187, A:F.190, E:I.67 CLA.2: 24 residues within 4Å: Chain A: W.185, G.189, F.190, G.197, S.200, H.201, A.204, A.205, L.208, W.247, V.251, T.255 Chain B: V.154, L.158, L.162 Chain E: F.57, I.64, L.65, Y.68 Ligands: CLA.1, CLA.3, CLA.9, BCR.37, LMG.38 15 PLIP interactions: 4 interactions with chain E, 8 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: E:F.57, E:L.65, E:L.65, E:Y.68, A:W.185, A:F.190, A:H.201, A:A.204, A:A.205, A:L.208, A:W.247, B:V.154, B:L.158, B:L.162 Metal complexes: A:H.201 CLA.3: 19 residues within 4Å: Chain A: R.68, L.69, S.146, L.149, C.150, F.153, H.201, H.202, W.247, A.248, V.251, A.262 Chain E: F.57, L.61 Ligands: CLA.2, CLA.4, CLA.5, CLA.6, CLA.9 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain E, Hydrophobic interactions: A:L.149, A:F.153, A:F.153, A:A.248, A:V.251, A:V.251, E:F.57, E:L.61 Salt bridges: A:R.68 Metal complexes: A:H.202 CLA.4: 23 residues within 4Å: Chain A: W.33, F.61, F.65, R.68, L.145, L.148, L.149, V.245, A.248, A.249, V.252, F.451, H.455, F.458, F.462 Ligands: CLA.3, CLA.5, CLA.7, CLA.10, CLA.11, CLA.12, CLA.13, CLA.15 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:W.33, A:F.61, A:F.65, A:L.145, A:L.148, A:L.149, A:A.248, A:A.249, A:V.252, A:F.451, A:F.458, A:F.458, A:F.458, A:F.462 Salt bridges: A:R.68 Metal complexes: A:H.455 CLA.5: 19 residues within 4Å: Chain A: T.27, V.30, W.33, A.34, V.62, F.65, M.66, L.69, V.96, H.100, L.103, G.147 Ligands: CLA.3, CLA.4, CLA.6, CLA.10, CLA.12, CLA.15, BCR.19 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:T.27, A:V.30, A:V.30, A:W.33, A:A.34, A:L.69, A:V.96, A:L.103 Metal complexes: A:H.100 CLA.6: 17 residues within 4Å: Chain A: L.69, I.71, W.91, G.95, A.98, A.99, H.100, G.152, F.153, F.156, H.157, F.162, G.163, P.164 Ligands: CLA.3, CLA.5, BCR.19 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:L.69, A:W.91, A:A.98, A:A.99, A:F.153, A:F.156, A:F.162 Metal complexes: A:H.157 CLA.7: 18 residues within 4Å: Chain A: W.33, M.37, F.40, Q.58, G.59, F.61, L.324, T.327, G.328, A.329, W.450, F.451 Chain H: F.32, I.36 Chain I: F.14 Ligands: CLA.4, BCR.17, LMG.20 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain H, Hydrophobic interactions: A:F.40, A:F.61, A:F.61, A:T.327, A:W.450, A:W.450, H:F.32, H:F.32, H:I.36 pi-Stacking: A:F.61 CLA.8: 19 residues within 4Å: Chain A: T.236, S.240, A.243, F.246, W.247, F.463, H.466, I.467, I.474 Chain B: F.120, M.126, L.127, I.150 Chain E: L.62 Ligands: CLA.9, CLA.10, LHG.23, LHG.32, LMG.38 10 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A, 1 interactions with chain E, Hydrophobic interactions: B:F.120, B:M.126, B:I.150, A:A.243, A:F.246, A:W.247, A:F.463, A:I.467, E:L.62 Metal complexes: A:H.466 CLA.9: 17 residues within 4Å: Chain A: F.139, L.143, L.208, A.212, F.215, H.216, P.221, L.229 Chain E: T.46, M.50, F.53 Ligands: CLA.2, CLA.3, CLA.8, CLA.10, LHG.23, BCR.37 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain E, Hydrophobic interactions: A:F.139, A:F.139, A:L.143, A:L.208, A:A.212, A:F.215, A:F.215, A:L.229, E:F.53 Metal complexes: A:H.216 CLA.10: 16 residues within 4Å: Chain A: L.19, H.23, L.135, F.139, H.142, L.143, M.231, V.237, S.240 Ligands: CLA.4, CLA.5, CLA.8, CLA.9, CLA.12, CLA.15, BCR.37 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:L.19, A:L.135, A:F.139, A:F.139 Hydrogen bonds: A:H.142 CLA.11: 19 residues within 4Å: Chain A: W.5, Y.6, R.7, H.9, T.10, L.238, L.461, F.462, F.464, G.465, W.468, H.469, R.472 Ligands: CLA.4, CLA.12, CLA.13, CLA.14, LHG.21, LHG.42 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:W.5, A:T.10, A:F.462, A:F.464 Salt bridges: A:R.472 pi-Stacking: A:W.468 Metal complexes: A:H.469 CLA.12: 18 residues within 4Å: Chain A: H.9, L.19, V.22, H.23, H.26, T.27, I.234, V.237, L.238, S.241, V.245 Ligands: CLA.4, CLA.5, CLA.10, CLA.11, CLA.13, CLA.14, CLA.15 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:L.19, A:V.22, A:I.234, A:V.237, A:V.245 Hydrogen bonds: A:S.241 Salt bridges: A:H.23 pi-Stacking: A:H.26 Metal complexes: A:H.23 CLA.13: 14 residues within 4Å: Chain A: H.9, H.26, L.29, V.30, L.461, F.462 Chain I: F.14 Ligands: CLA.4, CLA.11, CLA.12, CLA.14, BCR.18, LMG.20, LHG.21 7 PLIP interactions: 1 interactions with chain I, 6 interactions with chain A, Hydrophobic interactions: I:F.14, A:L.29, A:V.30, A:L.461, A:F.462 Salt bridges: A:H.9 Metal complexes: A:H.26 CLA.14: 13 residues within 4Å: Chain A: V.8, H.9, V.12, V.22, M.25, W.115 Chain H: Q.9, V.11 Chain I: F.21 Ligands: CLA.11, CLA.12, CLA.13, BCR.17 7 PLIP interactions: 4 interactions with chain A, 2 interactions with chain I, 1 interactions with chain H, Hydrophobic interactions: A:V.12, A:V.22, A:W.115, I:F.21, I:F.21 Metal complexes: A:H.9 Salt bridges: H:K.8 CLA.15: 14 residues within 4Å: Chain A: I.20, H.23, L.24, F.123, I.138, H.142, L.145 Chain E: N.34 Ligands: CLA.4, CLA.5, CLA.10, CLA.12, CLA.16, BCR.19 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:F.123, A:I.138, A:I.138, A:L.145, A:L.145 Hydrogen bonds: A:H.23 Metal complexes: A:H.142 CLA.16: 12 residues within 4Å: Chain A: L.24, A.110, W.113, H.114, L.120, L.122 Chain E: T.24, L.26, G.27, L.30 Ligands: CLA.15, BCR.19 9 PLIP interactions: 3 interactions with chain E, 6 interactions with chain A, Hydrophobic interactions: E:L.26, E:L.30, A:L.24, A:W.113, A:W.113, A:L.120, A:L.122 Hydrogen bonds: E:T.24 Metal complexes: A:H.114 CLA.25: 23 residues within 4Å: Chain B: L.122, P.149, V.152, V.156, I.182, F.185, Q.186, W.191, T.192, H.197, G.200, V.201, V.204, L.279, S.282, A.283, V.286 Chain O: M.174 Ligands: LMG.31, CLA.33, PHO.35, CLA.67, CLA.68 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:L.122, B:P.149, B:F.185, B:Q.186, B:V.201, B:V.204, B:L.279 pi-Stacking: B:W.191 Metal complexes: B:H.197 CLA.26: 19 residues within 4Å: Chain B: L.35, L.36, C.40, F.43, L.89, L.90, F.91, V.92, F.113, L.116, H.117, F.120 Chain E: L.62 Chain L: S.75, L.76, A.80 Ligands: LHG.23, LHG.32, BCR.37 12 PLIP interactions: 2 interactions with chain L, 9 interactions with chain B, 1 interactions with chain E, Hydrophobic interactions: L:L.76, L:L.76, B:L.36, B:F.43, B:F.91, B:F.91, B:L.116, B:F.120, E:L.62 Hydrogen bonds: B:V.92 pi-Stacking: B:F.113 Metal complexes: B:H.117 CLA.33: 16 residues within 4Å: Chain B: M.198, V.201, A.202, L.205 Chain O: T.36, I.40, F.149, M.163, I.167, T.170, M.174 Ligands: CLA.25, PL9.28, PHO.34, LHG.42, CLA.67 3 PLIP interactions: 2 interactions with chain O, 1 interactions with chain B, Hydrophobic interactions: O:I.40, O:F.149, B:V.201 CLA.46: 18 residues within 4Å: Chain N: L.83, L.156, G.159, A.160, L.163, H.225, E.232, M.270, I.273, A.274, M.277, A.284, Y.285 Ligands: CLA.47, CLA.48, CLA.51, CLA.52, BCR.59 8 PLIP interactions: 8 interactions with chain N, Hydrophobic interactions: N:L.163, N:L.163, N:I.273, N:I.273, N:A.274, N:A.284, N:Y.285 Metal complexes: N:H.225 CLA.47: 22 residues within 4Å: Chain N: W.51, L.76, H.79, Y.85, G.159, L.163, K.166, F.170, I.267, M.270, A.274, Y.285, L.414, H.418, L.421, F.425 Ligands: CLA.46, CLA.48, CLA.49, CLA.54, CLA.55, CLA.57 11 PLIP interactions: 11 interactions with chain N, Hydrophobic interactions: N:W.51, N:W.51, N:L.76, N:L.163, N:F.170, N:I.267, N:A.274, N:L.414, N:F.425 Salt bridges: N:H.79 Metal complexes: N:H.418 CLA.48: 16 residues within 4Å: Chain N: I.48, V.49, A.52, N.56, L.76, H.79, I.80, S.102, H.106 Ligands: LMG.45, CLA.46, CLA.47, CLA.52, CLA.54, CLA.55, CLA.57 3 PLIP interactions: 3 interactions with chain N, Hydrophobic interactions: N:V.49, N:A.52 Metal complexes: N:H.106 CLA.49: 16 residues within 4Å: Chain G: P.26, V.30 Chain N: W.51, M.55, F.58, G.73, I.75, W.413, S.417 Ligands: LMG.40, CLA.47, CLA.53, CLA.55, DGD.62, DGD.63, SQD.64 5 PLIP interactions: 4 interactions with chain N, 1 interactions with chain G, Hydrophobic interactions: N:I.75, N:I.75, N:W.413, N:W.413, G:V.30 CLA.50: 18 residues within 4Å: Chain F: F.19 Chain N: S.261, Y.262, G.265, A.266, V.269, F.426, H.429, L.430, A.433, R.437 Chain O: F.24, L.112, C.116 Ligands: CLA.52, BCR.59, LMG.65, CLA.69 11 PLIP interactions: 8 interactions with chain N, 1 interactions with chain F, 2 interactions with chain O, Hydrophobic interactions: N:Y.262, N:Y.262, N:V.269, N:F.426, N:L.430, F:F.19, O:F.24, O:L.112 Hydrogen bonds: N:Y.262 Salt bridges: N:R.437 Metal complexes: N:H.429 CLA.51: 17 residues within 4Å: Chain N: L.149, L.153, L.201, W.211, L.231, G.235, W.238, H.239, P.244, W.245, W.247, A.248, F.252 Ligands: CLA.46, CLA.52, BCR.59, LMG.65 9 PLIP interactions: 9 interactions with chain N, Hydrophobic interactions: N:L.149, N:L.153, N:L.153, N:W.211, N:W.247, N:F.252, N:F.252 Hydrogen bonds: N:W.245 Metal complexes: N:H.239 CLA.52: 18 residues within 4Å: Chain N: M.145, L.149, H.152, L.153, L.156, E.232, W.254, Y.259, Y.262, S.263, I.267, M.270 Ligands: CLA.46, CLA.48, CLA.50, CLA.51, CLA.54, BCR.59 9 PLIP interactions: 9 interactions with chain N, Hydrophobic interactions: N:M.145, N:L.149, N:L.156, N:W.254, N:Y.259, N:Y.259, N:Y.262, N:Y.262, N:Y.262 CLA.53: 16 residues within 4Å: Chain N: W.24, S.25, E.257, L.260, L.264, F.424, F.425, G.428, W.431, H.432, R.435 Ligands: LHG.30, CLA.49, CLA.54, CLA.55, CLA.56 7 PLIP interactions: 7 interactions with chain N, Hydrophobic interactions: N:L.260, N:F.425, N:W.431 Hydrogen bonds: N:S.25 Salt bridges: N:R.435 pi-Stacking: N:W.431 Metal complexes: N:H.432 CLA.54: 23 residues within 4Å: Chain N: N.27, L.30, I.31, L.37, A.40, H.41, H.44, Y.137, W.139, I.148, H.152, G.256, E.257, Y.259, L.260, S.263 Ligands: CLA.47, CLA.48, CLA.52, CLA.53, CLA.55, CLA.56, CLA.57 9 PLIP interactions: 9 interactions with chain N, Hydrophobic interactions: N:L.30, N:I.31, N:L.37, N:A.40, N:W.139, N:I.148, N:Y.259 Hydrogen bonds: N:S.263 Metal complexes: N:H.41 CLA.55: 15 residues within 4Å: Chain G: P.29, I.33 Chain N: N.27, H.44, L.47, I.48, W.51, F.424, F.425 Ligands: CLA.47, CLA.48, CLA.49, CLA.53, CLA.54, CLA.56 7 PLIP interactions: 7 interactions with chain N, Hydrophobic interactions: N:L.47, N:W.51, N:W.51, N:F.424, N:F.425 Hydrogen bonds: N:N.27 Metal complexes: N:H.44 CLA.56: 23 residues within 4Å: Chain G: F.32, I.33, L.35, W.39, Q.40 Chain M: V.20, V.23, P.24, A.28 Chain N: G.13, R.14, W.23, G.26, N.27, R.29, L.30, K.36, A.40, L.122 Ligands: CLA.53, CLA.54, CLA.55, BCR.60 18 PLIP interactions: 4 interactions with chain M, 6 interactions with chain G, 8 interactions with chain N, Hydrophobic interactions: M:V.20, M:V.23, M:P.24, M:A.28, G:F.32, G:I.33, G:L.35, G:W.39, G:W.39, N:W.23, N:L.30, N:K.36, N:A.40, N:L.122 pi-Stacking: G:W.39 Hydrogen bonds: N:R.14, N:R.29 Salt bridges: N:K.36 CLA.57: 17 residues within 4Å: Chain N: L.38, H.41, A.45, L.113, F.135, Y.137, Y.151, H.152, M.155, G.159, L.162, W.165 Ligands: BCR.44, CLA.47, CLA.48, CLA.54, CLA.58 7 PLIP interactions: 7 interactions with chain N, Hydrophobic interactions: N:H.41, N:F.135, N:Y.137, N:Y.151, N:L.162, N:W.165 Metal complexes: N:H.152 CLA.58: 13 residues within 4Å: Chain N: L.38, V.42, L.113, G.116, Y.119, H.120, P.125, L.128, Y.132, M.155, L.158 Ligands: BCR.44, CLA.57 9 PLIP interactions: 9 interactions with chain N, Hydrophobic interactions: N:L.38, N:L.38, N:V.42, N:L.113, N:Y.119, N:L.128, N:L.158 Hydrogen bonds: N:Y.119 Metal complexes: N:H.120 CLA.67: 22 residues within 4Å: Chain B: I.182 Chain O: P.141, A.144, M.174, F.177, Q.178, I.183, L.184, H.189, G.192, V.193, V.196, F.197, I.274, T.277, A.278, L.281 Ligands: CLA.25, LHG.29, CLA.33, PHO.34, CLA.68 12 PLIP interactions: 11 interactions with chain O, 1 interactions with chain B, Hydrophobic interactions: O:P.141, O:A.144, O:M.174, O:F.177, O:Q.178, O:I.183, O:I.183, O:L.184, O:L.184, O:V.196, B:I.182 Metal complexes: O:H.189 CLA.68: 11 residues within 4Å: Chain B: V.175, I.178, I.182 Chain O: M.190, V.193, A.194, F.197 Ligands: CLA.25, PHO.35, DGD.63, CLA.67 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain O, Hydrophobic interactions: B:I.182, O:V.193 CLA.69: 21 residues within 4Å: Chain F: F.7, V.8, Y.9, V.11, V.12, T.13, F.15, V.16 Chain O: I.27, C.31, F.84, P.86, I.87, W.88, Q.104, L.105, C.108, H.109, L.112 Ligands: CLA.50, LMG.65 10 PLIP interactions: 5 interactions with chain F, 5 interactions with chain O, Hydrophobic interactions: F:F.7, F:V.8, F:V.11, F:F.15, F:V.16, O:F.84, O:W.88, O:L.112 Hydrogen bonds: O:I.87 Metal complexes: O:H.109

10 x BCR: BETA-CAROTENE(Non-covalent)

BCR.17: 7 residues within 4Å: Chain A: M.25, W.115 Chain I: A.10 Ligands: CLA.7, CLA.14, BCR.18, LMG.20 3 PLIP interactions: 1 interactions with chain I, 2 interactions with chain A Hydrophobic interactions: I:A.10, A:W.115, A:W.115 BCR.18: 6 residues within 4Å: Chain A: S.36, I.101, G.105 Ligands: CLA.13, BCR.17, LMG.20 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.101 BCR.19: 9 residues within 4Å: Chain A: L.103, A.106, V.112, W.113, T.116 Ligands: CLA.5, CLA.6, CLA.15, CLA.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.103, A:A.106, A:V.112 BCR.27: 12 residues within 4Å: Chain B: Y.42, F.43, G.46, L.49, T.50, F.101, F.113 Chain D: P.28, T.29, F.32 Ligands: LMG.31, LMG.40 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:Y.42, B:F.43, B:L.49, B:F.101, B:F.113, D:P.28 BCR.37: 13 residues within 4Å: Chain E: M.50, F.53, I.54, F.57, F.60, L.74 Chain L: V.65, L.69 Ligands: CLA.1, CLA.2, CLA.9, CLA.10, CLA.26 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain L Hydrophobic interactions: E:F.53, E:I.54, E:F.57, E:F.57, E:F.57, E:F.60, E:L.74, L:V.65 BCR.39: 14 residues within 4Å: Chain G: L.25, I.28, F.31, L.34, L.35, V.38 Chain K: V.15, G.19 Chain M: I.13, S.16, F.17, V.20 Ligands: LHG.41, BCR.60 9 PLIP interactions: 1 interactions with chain K, 5 interactions with chain G, 3 interactions with chain M Hydrophobic interactions: K:V.15, G:L.25, G:I.28, G:F.31, G:L.34, G:L.35, M:I.13, M:V.20, M:V.20 BCR.44: 10 residues within 4Å: Chain M: G.55, N.58 Chain N: V.101, V.104, L.105, I.108, S.109, V.112 Ligands: CLA.57, CLA.58 6 PLIP interactions: 6 interactions with chain N Hydrophobic interactions: N:V.101, N:V.104, N:L.105, N:I.108, N:V.112, N:V.112 BCR.59: 14 residues within 4Å: Chain N: I.197, Y.200, L.201, I.212, V.215, D.220, I.221, G.224, I.228, F.252 Ligands: CLA.46, CLA.50, CLA.51, CLA.52 8 PLIP interactions: 8 interactions with chain N Hydrophobic interactions: N:I.197, N:Y.200, N:L.201, N:L.201, N:I.212, N:V.215, N:I.228, N:F.252 BCR.60: 17 residues within 4Å: Chain G: F.32, A.36, W.39 Chain M: L.9, L.12, I.13, S.16 Chain N: G.46, L.47, L.57, V.104, L.107, S.110, A.111, G.114 Ligands: BCR.39, CLA.56 12 PLIP interactions: 4 interactions with chain M, 4 interactions with chain G, 4 interactions with chain N Hydrophobic interactions: M:L.9, M:L.9, M:L.12, M:I.13, G:F.32, G:F.32, G:A.36, G:W.39, N:L.57, N:V.104, N:L.107, N:A.111 BCR.70: 10 residues within 4Å: Chain F: F.15 Chain O: W.11, I.29, L.33, T.34, V.38, I.41, A.45, L.93, L.97 8 PLIP interactions: 1 interactions with chain F, 7 interactions with chain O Hydrophobic interactions: F:F.15, O:W.11, O:I.29, O:I.29, O:L.33, O:L.33, O:V.38, O:I.41

6 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)

LMG.20: 15 residues within 4Å: Chain A: T.327, G.328, A.329, S.332, F.453, C.457, F.458 Chain H: I.36 Chain I: Y.6, G.7, F.14 Ligands: CLA.7, CLA.13, BCR.17, BCR.18 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: A:F.453, A:F.458, I:F.14 Hydrogen bonds: A:T.327, A:T.327, A:A.329, A:S.332 LMG.31: 11 residues within 4Å: Chain B: Y.67, C.71, N.72, F.73 Chain D: I.36, M.39, Q.40, R.44 Ligands: CLA.25, BCR.27, DGD.63 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:M.39, D:Q.40, B:N.72, B:F.73 Hydrophobic interactions: B:F.73 LMG.38: 17 residues within 4Å: Chain A: Y.193, F.246, G.254, Y.258, Q.277, T.452, V.456, F.463 Chain B: A.86, H.87, I.123, L.162, L.291 Chain E: Y.68, N.69 Ligands: CLA.2, CLA.8 10 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: A:F.246, A:T.452, A:V.456, A:F.463, B:L.291, E:Y.68, E:Y.68 Hydrogen bonds: A:Y.193, A:Q.277 Salt bridges: B:H.87 LMG.40: 8 residues within 4Å: Chain G: V.27, V.30 Chain K: T.8, L.12 Chain N: H.62 Ligands: BCR.27, CLA.49, DGD.62 3 PLIP interactions: 1 interactions with chain K, 2 interactions with chain G Hydrophobic interactions: K:L.12, G:V.27, G:V.30 LMG.45: 10 residues within 4Å: Chain N: G.84, Y.85, G.86, D.95, P.98, S.102, L.105, H.106, S.109 Ligands: CLA.48 5 PLIP interactions: 5 interactions with chain N Hydrophobic interactions: N:Y.85, N:P.98, N:L.105 Hydrogen bonds: N:G.86, N:D.95 LMG.65: 17 residues within 4Å: Chain F: K.5, Y.9 Chain N: V.202, S.204, F.206, D.209, W.211 Chain O: F.84, W.88, E.89, C.108, L.111, Y.115 Ligands: CLA.50, CLA.51, DGD.61, CLA.69 7 PLIP interactions: 3 interactions with chain O, 2 interactions with chain F, 2 interactions with chain N Hydrophobic interactions: O:L.111, O:Y.115, N:W.211 Hydrogen bonds: O:W.88, F:Y.9, F:Y.9, N:S.204

8 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)

LHG.21: 14 residues within 4Å: Chain A: Y.6, R.7, W.468 Chain B: Y.141, I.144, W.266, F.269, L.273, V.276, T.277, W.280 Ligands: CLA.11, CLA.13, LHG.42 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.273, B:V.276, B:T.277 Hydrogen bonds: B:Y.141 Salt bridges: A:R.7 LHG.22: 13 residues within 4Å: Chain A: R.224, G.228 Chain B: F.15, D.19, R.23, W.32, E.131 Chain E: W.44, M.50, A.51 Chain L: A.87, I.90 Ligands: LHG.23 8 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 2 interactions with chain E, 2 interactions with chain L Hydrophobic interactions: B:F.15, B:W.32, E:W.44, E:A.51, L:A.87, L:I.90 Hydrogen bonds: B:R.23 Salt bridges: A:R.224 LHG.23: 11 residues within 4Å: Chain A: G.228 Chain B: R.23, L.36, E.131, R.134 Chain L: L.83 Ligands: CLA.8, CLA.9, LHG.22, CLA.26, LHG.32 3 PLIP interactions: 1 interactions with chain L, 2 interactions with chain B Hydrophobic interactions: L:L.83, B:L.36 Hydrogen bonds: B:R.23 LHG.29: 22 residues within 4Å: Chain B: I.256, F.257, V.259, A.260, F.261, S.262, N.263, W.266 Chain H: N.14, T.16, Y.19, W.20 Chain J: L.10, T.13, L.14, I.17, S.20, I.21 Ligands: PL9.28, PHO.34, LHG.42, CLA.67 17 PLIP interactions: 4 interactions with chain H, 7 interactions with chain B, 6 interactions with chain J Hydrophobic interactions: H:Y.19, H:W.20, H:W.20, B:F.257, B:F.257, B:V.259, B:F.261, J:L.10, J:L.14, J:I.17, J:I.17, J:I.21, J:I.21 Hydrogen bonds: H:T.16, B:S.262, B:S.262, B:N.263 LHG.30: 14 residues within 4Å: Chain B: E.219, N.220, A.229, N.230, T.231, F.232 Chain N: W.24, S.25, W.431, R.435 Chain O: R.131, W.133, F.264 Ligands: CLA.53 8 PLIP interactions: 2 interactions with chain B, 2 interactions with chain O, 4 interactions with chain N Hydrogen bonds: B:N.220, B:T.231, N:S.25, N:S.25 Hydrophobic interactions: O:F.264, N:W.24, N:W.431 Salt bridges: O:R.131 LHG.32: 13 residues within 4Å: Chain B: V.92, W.93, Q.98, G.99 Chain L: P.67, K.70, N.71, G.74, A.78, L.83 Ligands: CLA.8, LHG.23, CLA.26 6 PLIP interactions: 3 interactions with chain L, 3 interactions with chain B Hydrophobic interactions: L:L.83, B:V.92, B:W.93 Hydrogen bonds: L:N.71, B:Q.98 Salt bridges: L:K.70 LHG.41: 6 residues within 4Å: Chain G: S.44, F.45 Chain N: W.23 Chain P: V.66 Ligands: BCR.39, SQD.64 3 PLIP interactions: 1 interactions with chain P, 2 interactions with chain G Hydrophobic interactions: P:V.66 Hydrogen bonds: G:S.44, G:S.44 LHG.42: 19 residues within 4Å: Chain A: W.5, Y.6 Chain B: W.266, F.270, L.273 Chain H: N.14, S.17, W.20, G.21, L.23, L.24, V.27 Chain I: I.17, F.21 Ligands: CLA.11, LHG.21, PL9.28, LHG.29, CLA.33 15 PLIP interactions: 2 interactions with chain A, 3 interactions with chain I, 8 interactions with chain H, 2 interactions with chain B Hydrophobic interactions: A:W.5, I:I.17, I:F.21, I:F.21, H:W.20, H:W.20, H:L.23, H:L.24, H:V.27, B:F.270, B:L.273 Hydrogen bonds: A:Y.6, H:N.14, H:S.17, H:S.17

1 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.24: 8 residues within 4Å: Chain B: H.214, E.242, Y.244, H.268 Chain O: H.206, N.238, H.263 Ligands: FE2.66 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain O Hydrogen bonds: B:Y.244, O:N.238

1 x PL9: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE(Non-covalent)

PL9.28: 22 residues within 4Å: Chain B: M.198, M.199, G.203, L.209, L.210, I.213, H.214, T.217, W.253, V.259, A.260, F.261 Chain H: V.27, V.30 Chain J: L.10 Chain O: F.39, F.43, I.68, I.167 Ligands: LHG.29, CLA.33, LHG.42 15 PLIP interactions: 1 interactions with chain H, 4 interactions with chain O, 8 interactions with chain B, 2 interactions with chain J Hydrophobic interactions: H:V.30, O:F.39, O:F.43, O:I.68, O:I.167, B:M.199, B:L.209, B:L.210, B:I.213, B:F.261, B:F.261, J:L.10, J:L.10 Hydrogen bonds: B:T.217, B:F.261

2 x PHO: PHEOPHYTIN A(Non-covalent)

PHO.34: 22 residues within 4Å: Chain B: L.205, L.209, I.213, W.253, F.257 Chain O: L.32, A.35, T.36, F.39, F.110, Y.117, E.121, A.137, Y.138, A.140, P.141, L.165, G.166, I.274 Ligands: LHG.29, CLA.33, CLA.67 12 PLIP interactions: 9 interactions with chain O, 3 interactions with chain B Hydrophobic interactions: O:L.32, O:A.35, O:F.39, O:F.110, O:Y.138, O:A.140, O:P.141, O:L.165, O:I.274, B:L.205, B:I.213, B:I.213 PHO.35: 22 residues within 4Å: Chain B: A.41, L.45, W.48, G.118, L.122, F.125, Q.129, N.142, A.145, F.146, A.148, P.149, F.153, G.174, L.279 Chain O: F.197, S.200, L.201, M.205, I.250 Ligands: CLA.25, CLA.68 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain O Hydrophobic interactions: B:A.41, B:L.45, B:W.48, B:W.48, B:L.122, B:F.125, B:A.145, B:F.146, B:A.148, B:F.153, B:L.279, O:F.197, O:L.201 Hydrogen bonds: B:N.142 pi-Stacking: B:F.146

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

HEM.36: 18 residues within 4Å: Chain C: R.8, I.13, R.18, Y.19, I.22, H.23, T.26, V.27, L.30 Chain D: I.14, R.18, W.19, I.22, H.23, A.26, V.27, I.30 Chain P: I.63 18 PLIP interactions: 8 interactions with chain D, 9 interactions with chain C, 1 interactions with chain P, Hydrophobic interactions: D:I.22, D:A.26, D:V.27, D:I.30, C:I.13, C:I.22, C:I.22, C:T.26, C:V.27, C:L.30, P:I.63 Salt bridges: D:R.18, C:R.8, C:R.18 pi-Stacking: D:W.19, C:Y.19 pi-Cation interactions: D:H.23 Metal complexes: D:H.23

1 x VTQ: RRR-ALPHA-TOCOPHERYLQUINONE(Non-covalent)

VTQ.43: 12 residues within 4Å: Chain B: R.26, V.28, L.35, F.38 Chain D: F.15, T.16, V.17, L.20, A.21 Chain L: I.90, V.93, D.97 11 PLIP interactions: 4 interactions with chain B, 4 interactions with chain D, 3 interactions with chain L Hydrophobic interactions: B:V.28, B:L.35, B:F.38, B:F.38, D:L.20, D:A.21, L:I.90, L:V.93, L:V.93 Hydrogen bonds: D:T.16, D:V.17

3 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)

DGD.61: 23 residues within 4Å: Chain N: P.205, G.207, G.208, G.210, W.211, C.213, S.214, V.215, F.272, C.276, N.281, N.282, T.283, D.348, F.349, R.350, F.423, F.426 Chain O: L.82, Y.115, S.146, I.154 Ligands: LMG.65 14 PLIP interactions: 13 interactions with chain N, 1 interactions with chain O Hydrophobic interactions: N:F.272, N:F.423, N:F.423, N:F.426, O:I.154 Hydrogen bonds: N:G.208, N:W.211, N:V.215, N:N.282, N:T.283, N:D.348, N:D.348, N:R.350, N:R.350 DGD.62: 8 residues within 4Å: Chain N: E.71, Q.72, S.394, V.408, W.413 Ligands: LMG.40, CLA.49, DGD.63 5 PLIP interactions: 5 interactions with chain N Hydrophobic interactions: N:W.413, N:W.413 Hydrogen bonds: N:S.394, N:S.394, N:V.408 DGD.63: 13 residues within 4Å: Chain B: N.72 Chain N: L.392, N.393 Chain O: M.190, A.194, F.291, N.292, F.293, S.296 Ligands: LMG.31, CLA.49, DGD.62, CLA.68 5 PLIP interactions: 2 interactions with chain N, 3 interactions with chain O Hydrophobic interactions: N:L.392, O:A.194, O:F.291 Hydrogen bonds: N:N.393, O:N.292

1 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)

SQD.64: 15 residues within 4Å: Chain B: N.230, F.232, R.233 Chain G: F.37 Chain N: A.22, W.24 Chain O: N.258, S.261, F.264, F.265, A.268, W.269, I.272 Ligands: LHG.41, CLA.49 14 PLIP interactions: 10 interactions with chain O, 2 interactions with chain B, 1 interactions with chain N, 1 interactions with chain G Hydrophobic interactions: O:F.264, O:F.265, O:A.268, O:W.269, O:W.269, O:W.269, O:I.272, N:W.24, G:F.37 Hydrogen bonds: O:N.258, O:S.261, O:S.261, B:N.230 Salt bridges: B:R.233

1 x FE2: FE (II) ION(Non-covalent)

FE2.66: 5 residues within 4Å: Chain B: H.214, H.268 Chain O: H.206, H.263 Ligands: BCT.24 4 PLIP interactions: 2 interactions with chain O, 2 interactions with chain B Metal complexes: O:H.206, O:H.263, B:H.214, B:H.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, A. et al., Structural basis for an early stage of the photosystem II repair cycle in Chlamydomonas reinhardtii. Nat Commun (2024)

Release Date

2024-06-19

Peptides

Photosystem II CP47 reaction center protein: A
Photosystem II D2 protein: B
Cytochrome b559 subunit alpha: C
Cytochrome b559 subunit beta: D
Photosystem II reaction center protein H: E
Photosystem II reaction center protein I: F
Photosystem II reaction center protein K: G
Photosystem II reaction center protein L: H
Photosystem II reaction center protein M: I
Photosystem II reaction center protein T: J
Photosystem II reaction center protein Psb30: K
4.1 kDa photosystem II subunit: L
Photosystem II reaction center protein Z: M
Photosystem II CP43 reaction center protein: N
Photosystem II protein D1: O
Chains: 1: P

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
E

D
F

E
H

F
I

G
K

H
L

I
M

J
T

K
V

L
X

M
Z

N
C

O
A

P
1

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Photosystem II CP47 reaction center protein

Photosystem II D2 protein

Cytochrome b559 subunit alpha

Cytochrome b559 subunit beta

Photosystem II reaction center protein H

Photosystem II reaction center protein I

Photosystem II reaction center protein K

Photosystem II reaction center protein L

Photosystem II reaction center protein M

Photosystem II reaction center protein T

Photosystem II reaction center protein Psb30

4.1 kDa photosystem II subunit

Photosystem II reaction center protein Z

Photosystem II CP43 reaction center protein

Photosystem II protein D1

Chains: 1

Related Entries With Identical Sequence