SMTL ID : 8kde.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

35 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.1: 10 residues within 4Å: Chain A: W.185, G.186, A.187, F.190 Chain E: I.63, I.67, L.74 Ligands: CLA.2, LHG.24, BCR.37 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain A, Hydrophobic interactions: E:I.63, E:I.67, E:L.74, A:A.187, A:F.190 CLA.2: 26 residues within 4Å: Chain A: W.185, G.189, F.190, P.192, G.197, S.200, H.201, A.204, L.208, W.247, F.250, V.251, T.255 Chain B: V.154, L.158, L.162 Chain E: F.57, F.60, I.64, L.65, Y.68 Ligands: CLA.1, CLA.3, CLA.9, LMG.23, BCR.37 19 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B, 6 interactions with chain E, Hydrophobic interactions: A:W.185, A:F.190, A:F.190, A:P.192, A:H.201, A:A.204, A:L.208, A:W.247, A:F.250, B:V.154, B:L.158, B:L.162, E:F.57, E:F.60, E:I.64, E:L.65, E:L.65, E:Y.68 Metal complexes: A:H.201 CLA.3: 25 residues within 4Å: Chain A: R.68, L.69, S.146, L.149, C.150, F.153, I.166, I.198, H.201, H.202, W.247, A.248, V.251, V.252, A.262 Chain E: I.54, F.57, L.61 Ligands: CLA.2, CLA.4, CLA.5, CLA.6, CLA.8, CLA.9, CLA.10 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain E, Hydrophobic interactions: A:L.149, A:F.153, A:F.153, A:A.248, A:V.251, A:V.251, A:V.252, E:I.54, E:F.57, E:L.61 Hydrogen bonds: A:R.68 Salt bridges: A:R.68 pi-Cation interactions: A:H.201 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 19 PLIP interactions: 19 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:L.149, A:A.248, A:A.249, A:V.252, A:V.252, A:F.451, A:F.458, A:F.458, A:F.458, A:F.458, A:F.462 Salt bridges: A:R.68 Metal complexes: A:H.455 CLA.5: 21 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, L.143, S.146, G.147 Ligands: CLA.3, CLA.4, CLA.6, CLA.10, CLA.12, CLA.15, BCR.19 10 PLIP interactions: 10 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, A:L.143 Metal complexes: A:H.100 CLA.6: 18 residues within 4Å: Chain A: L.69, I.71, I.90, W.91, A.98, A.99, I.102, L.149, G.152, F.153, F.156, H.157, F.162, G.163, P.164 Ligands: CLA.3, CLA.5, BCR.19 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:L.69, A:L.69, A:I.90, A:W.91, A:A.98, A:A.99, A:I.102, A:L.149, A:F.153, A:F.156, A:F.162, A:F.162 Metal complexes: A:H.157 CLA.7: 22 residues within 4Å: Chain A: W.33, M.37, F.40, Q.58, G.59, M.60, F.61, L.324, T.327, G.328, A.329, W.450, F.451 Chain B: F.196 Chain H: F.32, I.36 Chain I: F.14 Ligands: CLA.4, CLA.13, BCR.17, BCR.18, LMG.20 7 PLIP interactions: 4 interactions with chain A, 2 interactions with chain H, 1 interactions with chain B, Hydrophobic interactions: A:F.61, A:T.327, A:W.450, H:F.32, H:I.36, B:F.196 pi-Stacking: A:F.61 CLA.8: 23 residues within 4Å: Chain A: T.236, S.239, S.240, A.243, W.247, F.463, H.466, I.467, I.474 Chain B: L.36, F.120, I.123, M.126, L.127, I.150 Chain E: L.62 Ligands: CLA.3, CLA.9, CLA.10, LHG.22, LMG.23, CLA.26, LHG.42 13 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B, 1 interactions with chain E, Hydrophobic interactions: A:A.243, A:W.247, A:W.247, A:F.463, A:I.467, B:L.36, B:F.120, B:I.123, B:M.126, B:L.127, B:I.150, E:L.62 Metal complexes: A:H.466 CLA.9: 20 residues within 4Å: Chain A: F.139, L.143, L.208, A.212, F.215, H.216, P.221, L.229, M.231 Chain E: T.46, M.50, F.53, I.54 Ligands: CLA.2, CLA.3, CLA.8, CLA.10, LHG.21, LHG.22, BCR.37 13 PLIP interactions: 10 interactions with chain A, 3 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:M.50, E:F.53, E:I.54 Salt bridges: A:H.216 Metal complexes: A:H.216 CLA.10: 19 residues within 4Å: Chain A: L.19, H.23, L.135, F.139, H.142, L.143, S.146, L.229, M.231, V.237, S.240 Ligands: CLA.3, CLA.4, CLA.5, CLA.8, CLA.9, CLA.12, CLA.15, BCR.37 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:L.19, A:L.135, A:F.139, A:F.139, A:L.229 Hydrogen bonds: A:H.142 CLA.11: 21 residues within 4Å: Chain A: W.5, Y.6, R.7, V.8, H.9, T.10, L.238, I.242, L.461, F.462, F.464, G.465, W.468, H.469, R.472 Ligands: CLA.4, CLA.12, CLA.13, CLA.14, LHG.29, LHG.41 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:W.5, A:T.10, A:L.238, A:I.242, A:F.462, A:F.464 Salt bridges: A:H.9, A:R.472 pi-Stacking: A:W.468 Metal complexes: A:H.469 CLA.12: 20 residues within 4Å: Chain A: H.9, L.19, V.22, H.23, H.26, T.27, I.234, E.235, V.237, L.238, S.241, I.242, V.245 Ligands: CLA.4, CLA.5, CLA.10, CLA.11, CLA.13, CLA.14, CLA.15 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:H.9, A:L.19, A:V.22, A:I.234, A:V.237, A:L.238, A:L.238, 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: 17 residues within 4Å: Chain A: H.9, H.26, L.29, V.30, W.33, L.461, F.462 Chain I: F.14 Ligands: CLA.4, CLA.7, CLA.11, CLA.12, CLA.14, BCR.17, BCR.18, LMG.20, LHG.29 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain I, Hydrophobic interactions: A:L.29, A:V.30, A:W.33, A:W.33, A:L.461, A:F.462, I:F.14 Salt bridges: A:H.9 Metal complexes: A:H.26 CLA.14: 15 residues within 4Å: Chain A: V.8, H.9, V.11, V.12, V.22, M.25, L.29, W.115 Chain H: Q.9, V.11 Chain I: F.21 Ligands: CLA.11, CLA.12, CLA.13, BCR.17 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain I, Hydrophobic interactions: A:V.8, A:V.12, A:V.22, A:V.22, A:M.25, A:L.29, A:W.115, I:F.21, I:F.21 Metal complexes: A:H.9 CLA.15: 16 residues within 4Å: Chain A: I.20, H.23, L.24, F.123, I.138, I.141, H.142, L.145 Chain E: L.33, N.34 Ligands: CLA.4, CLA.5, CLA.10, CLA.12, CLA.16, BCR.19 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain E, Hydrophobic interactions: A:F.123, A:I.138, A:I.138, A:I.141, A:L.145, A:L.145, E:L.33 Hydrogen bonds: A:H.23 Metal complexes: A:H.142 CLA.16: 13 residues within 4Å: Chain A: I.20, 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: 7 interactions with chain A, 2 interactions with chain E, Hydrophobic interactions: A:I.20, A:L.24, A:W.113, A:L.120, A:L.122, E:L.30 pi-Stacking: A:W.113 Metal complexes: A:H.114 Hydrogen bonds: E:T.24 CLA.25: 22 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 Ligands: LMG.32, CLA.33, PHO.35, CLA.67, CLA.68 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:L.122, B:P.149, B:V.152, B:I.182, B:F.185, B:Q.186, B:W.191, B:T.192, B:V.201, B:V.204, B:L.279 pi-Stacking: B:W.191 Metal complexes: B:H.197 CLA.26: 25 residues within 4Å: Chain B: L.35, L.36, C.40, F.43, L.89, L.90, F.91, V.92, W.93, W.104, A.112, F.113, L.116, H.117, F.120 Chain E: L.55, L.56, L.62 Chain L: S.75, L.76, A.80 Ligands: CLA.8, LHG.22, BCR.37, LHG.42 15 PLIP interactions: 2 interactions with chain E, 11 interactions with chain B, 2 interactions with chain L, Hydrophobic interactions: E:L.56, E:L.62, B:L.36, B:F.43, B:F.43, B:F.91, B:F.91, B:W.93, B:L.116, B:F.120, L:L.76, L:A.80 Hydrogen bonds: B:V.92 pi-Stacking: B:F.113 Metal complexes: B:H.117 CLA.33: 19 residues within 4Å: Chain B: M.198, V.201, A.202, L.205, G.206 Chain Q: T.45, I.49, V.157, F.158, M.172, I.176, T.179, F.180, M.183 Ligands: CLA.25, PL9.28, PHO.34, LHG.41, CLA.67 5 PLIP interactions: 4 interactions with chain Q, 1 interactions with chain B, Hydrophobic interactions: Q:I.49, Q:V.157, Q:F.158, Q:F.180, B:V.201 CLA.46: 21 residues within 4Å: Chain P: L.83, L.156, G.159, A.160, L.163, I.212, M.218, H.225, I.228, 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 9 PLIP interactions: 9 interactions with chain P, Hydrophobic interactions: P:L.156, P:L.163, P:I.212, P:I.228, P:I.273, P:I.273, P:A.284, P:Y.285 Metal complexes: P:H.225 CLA.47: 23 residues within 4Å: Chain P: W.51, I.75, L.76, H.79, Y.85, G.159, L.162, K.166, I.267, M.270, A.274, Y.285, L.414, H.418, L.421, F.425 Ligands: LMG.39, CLA.46, CLA.48, CLA.49, CLA.54, CLA.55, CLA.57 12 PLIP interactions: 12 interactions with chain P, Hydrophobic interactions: P:W.51, P:W.51, P:I.75, P:L.76, P:L.162, P:I.267, P:A.274, P:L.414, P:F.425 Salt bridges: P:H.79, P:H.418 Metal complexes: P:H.418 CLA.48: 17 residues within 4Å: Chain P: I.48, V.49, A.52, L.76, H.79, I.80, L.83, S.102, H.106, I.267 Ligands: LMG.45, CLA.46, CLA.47, CLA.52, CLA.54, CLA.55, CLA.57 6 PLIP interactions: 6 interactions with chain P, Hydrophobic interactions: P:I.48, P:V.49, P:A.52, P:L.83, P:I.267 Metal complexes: P:H.106 CLA.49: 18 residues within 4Å: Chain G: P.26, V.30 Chain P: W.51, M.55, F.58, G.73, I.75, W.413, S.417 Chain Q: F.197 Ligands: LMG.39, CLA.47, CLA.53, CLA.55, DGD.62, DGD.63, SQD.64, LHG.72 7 PLIP interactions: 1 interactions with chain G, 5 interactions with chain P, 1 interactions with chain Q, Hydrophobic interactions: G:V.30, P:F.58, P:I.75, P:I.75, P:W.413, P:W.413, Q:F.197 CLA.50: 24 residues within 4Å: Chain F: V.16, F.19, F.23 Chain P: F.252, S.261, Y.262, G.265, A.266, V.269, F.426, H.429, L.430, A.433, R.437 Chain Q: F.33, L.121, Y.124, C.125, G.128, W.131 Ligands: CLA.52, BCR.59, CLA.69, LMG.71 17 PLIP interactions: 9 interactions with chain P, 5 interactions with chain Q, 3 interactions with chain F, Hydrophobic interactions: P:Y.262, P:Y.262, P:V.269, P:F.426, P:L.430, P:A.433, Q:F.33, Q:L.121, Q:Y.124, Q:W.131, Q:W.131, F:V.16, F:F.19, F:F.23 Hydrogen bonds: P:Y.262 Salt bridges: P:R.437 Metal complexes: P:H.429 CLA.51: 18 residues within 4Å: Chain P: L.149, L.153, L.201, W.211, L.231, G.235, W.238, H.239, T.242, P.244, W.245, W.247, A.248, F.252 Ligands: CLA.46, CLA.52, BCR.59, LMG.71 10 PLIP interactions: 10 interactions with chain P, Hydrophobic interactions: P:L.149, P:L.153, P:L.153, P:W.211, P:W.238, P:W.247, P:F.252, P:F.252 Hydrogen bonds: P:W.245 Metal complexes: P:H.239 CLA.52: 21 residues within 4Å: Chain P: M.145, T.146, I.148, L.149, H.152, L.153, L.156, E.232, F.252, W.254, Y.259, Y.262, S.263, A.266, M.270 Ligands: CLA.46, CLA.48, CLA.50, CLA.51, CLA.54, BCR.59 12 PLIP interactions: 12 interactions with chain P, Hydrophobic interactions: P:M.145, P:I.148, P:L.149, P:L.156, P:F.252, P:W.254, P:Y.259, P:Y.259, P:Y.262, P:Y.262, P:Y.262, P:A.266 CLA.53: 19 residues within 4Å: Chain P: W.24, S.25, A.28, E.257, L.260, L.264, L.421, F.424, F.425, G.428, W.431, H.432, R.435 Ligands: LHG.31, CLA.49, CLA.54, CLA.55, CLA.56, SQD.64 7 PLIP interactions: 7 interactions with chain P, Hydrophobic interactions: P:L.421, P:F.424, P:F.425, P:W.431 Salt bridges: P:R.435 pi-Stacking: P:W.431 Metal complexes: P:H.432 CLA.54: 25 residues within 4Å: Chain P: 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, L.264, I.267 Ligands: CLA.47, CLA.48, CLA.52, CLA.53, CLA.55, CLA.56, CLA.57 10 PLIP interactions: 10 interactions with chain P, Hydrophobic interactions: P:N.27, P:L.30, P:I.31, P:L.37, P:A.40, P:W.139, P:I.148, P:Y.259 Hydrogen bonds: P:S.263 Metal complexes: P:H.41 CLA.55: 16 residues within 4Å: Chain G: P.29, V.30, I.33 Chain P: 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 10 PLIP interactions: 2 interactions with chain G, 8 interactions with chain P, Hydrophobic interactions: G:P.29, G:V.30, P:L.47, P:I.48, P:W.51, P:W.51, P:F.424, P:F.425 Hydrogen bonds: P:N.27 Metal complexes: P:H.44 CLA.56: 26 residues within 4Å: Chain G: F.32, I.33, L.35, W.39, Q.40 Chain K: V.22, L.26 Chain M: V.20, V.23, P.24, A.28 Chain P: G.13, R.14, W.23, G.26, N.27, R.29, L.30, L.33, K.36, A.40, L.122 Ligands: CLA.53, CLA.54, CLA.55, BCR.60 19 PLIP interactions: 3 interactions with chain M, 7 interactions with chain P, 7 interactions with chain G, 2 interactions with chain K, Hydrophobic interactions: M:V.23, M:P.24, M:A.28, P:L.30, P:K.36, P:A.40, P:L.122, G:F.32, G:I.33, G:L.35, G:W.39, G:W.39, G:W.39, K:V.22, K:L.26 Hydrogen bonds: P:R.14, P:R.29 Salt bridges: P:K.36 pi-Stacking: G:W.39 CLA.57: 18 residues within 4Å: Chain P: H.41, A.45, L.113, F.135, Y.137, I.148, Y.151, H.152, M.155, L.156, L.158, G.159, L.162 Ligands: BCR.44, CLA.47, CLA.48, CLA.54, CLA.58 8 PLIP interactions: 8 interactions with chain P, Hydrophobic interactions: P:H.41, P:F.135, P:Y.137, P:I.148, P:Y.151, P:L.158, P:L.162 Metal complexes: P:H.152 CLA.58: 14 residues within 4Å: Chain P: L.38, V.42, V.112, L.113, F.115, G.116, Y.119, H.120, P.125, L.128, Y.132, F.135 Ligands: BCR.44, CLA.57 11 PLIP interactions: 11 interactions with chain P, Hydrophobic interactions: P:L.38, P:V.42, P:V.112, P:L.113, P:F.115, P:Y.119, P:L.128, P:Y.132, P:F.135 pi-Stacking: P:Y.119 Metal complexes: P:H.120 CLA.67: 27 residues within 4Å: Chain B: I.182, L.205 Chain Q: F.119, Y.147, P.150, A.153, A.154, V.157, M.183, F.186, Q.187, I.192, L.193, H.198, G.201, V.202, V.205, F.206, I.283, T.286, A.287, L.290 Ligands: CLA.25, LHG.30, CLA.33, PHO.34, CLA.68 14 PLIP interactions: 12 interactions with chain Q, 2 interactions with chain B, Hydrophobic interactions: Q:F.119, Q:P.150, Q:A.153, Q:F.186, Q:Q.187, Q:I.192, Q:I.192, Q:L.193, Q:V.205, Q:F.206, Q:F.206, B:I.182, B:L.205 Metal complexes: Q:H.198 CLA.68: 14 residues within 4Å: Chain B: V.175, I.178, F.179, I.182 Chain Q: M.199, V.202, A.203, F.206, G.207 Ligands: CLA.25, PHO.35, DGD.63, CLA.67, LHG.72 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain Q, Hydrophobic interactions: B:F.179, B:I.182, B:I.182, Q:V.202 CLA.69: 23 residues within 4Å: Chain F: F.7, V.8, Y.9, V.11, V.12, T.13, F.15 Chain Q: I.36, P.39, C.40, T.43, F.93, P.95, I.96, W.97, Q.113, L.114, C.117, H.118, L.121 Ligands: CLA.50, BCR.70, LMG.71 14 PLIP interactions: 5 interactions with chain F, 9 interactions with chain Q, Hydrophobic interactions: F:F.7, F:Y.9, F:V.11, F:V.12, F:F.15, Q:P.39, Q:P.39, Q:F.93, Q:P.95, Q:I.96, Q:W.97, Q:L.121 Hydrogen bonds: Q:I.96 Metal complexes: Q:H.118

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

BCR.17: 11 residues within 4Å: Chain A: M.25, L.29, S.111, V.112, W.115 Chain I: A.10 Ligands: CLA.7, CLA.13, CLA.14, BCR.18, LMG.20 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: A:L.29, A:W.115, A:W.115, I:A.10 BCR.18: 8 residues within 4Å: Chain A: L.29, G.32, I.101, G.105 Ligands: CLA.7, CLA.13, BCR.17, LMG.20 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.29, A:I.101 BCR.19: 10 residues within 4Å: Chain A: L.103, A.106, L.109, 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, F.101, F.113 Chain D: P.28, T.29, F.32 Ligands: LMG.32, LMG.39, LHG.42 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:P.28, D:T.29, D:F.32, B:Y.42, B:F.43, B:L.49, B:F.101, B:F.113 BCR.37: 12 residues within 4Å: Chain E: M.50, F.53, I.54, F.57, F.60 Chain L: V.65, L.69 Ligands: CLA.1, CLA.2, CLA.9, CLA.10, CLA.26 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain L Hydrophobic interactions: E:F.53, E:I.54, E:F.57, E:F.57, E:F.57, E:F.60, L:V.65, L:L.69 BCR.38: 16 residues within 4Å: Chain G: I.21, L.25, I.28, F.31, L.34, L.35, F.37, V.38 Chain K: V.15, G.19 Chain M: I.13, S.16, F.17, V.20 Ligands: LHG.40, BCR.60 12 PLIP interactions: 8 interactions with chain G, 1 interactions with chain K, 3 interactions with chain M Hydrophobic interactions: G:I.21, G:L.25, G:I.28, G:F.31, G:F.31, G:L.34, G:L.35, G:F.37, K:V.15, M:I.13, M:F.17, M:V.20 BCR.44: 12 residues within 4Å: Chain M: F.52, G.55, N.58 Chain P: V.101, V.104, L.105, I.108, S.109, V.112, F.135 Ligands: CLA.57, CLA.58 8 PLIP interactions: 7 interactions with chain P, 1 interactions with chain M Hydrophobic interactions: P:V.101, P:V.104, P:I.108, P:V.112, P:V.112, P:F.135, P:F.135, M:F.52 BCR.59: 17 residues within 4Å: Chain F: F.23, L.24 Chain P: I.197, F.198, 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 12 PLIP interactions: 10 interactions with chain P, 2 interactions with chain F Hydrophobic interactions: P:I.197, P:F.198, P:Y.200, P:L.201, P:L.201, P:L.201, P:I.212, P:V.215, P:I.228, P:F.252, F:F.23, F:L.24 BCR.60: 17 residues within 4Å: Chain G: I.21, F.32, A.36, W.39 Chain M: L.9, L.12, I.13, S.16 Chain P: G.46, L.47, L.57, L.107, S.110, A.111, G.114 Ligands: BCR.38, CLA.56 10 PLIP interactions: 5 interactions with chain G, 3 interactions with chain M, 2 interactions with chain P Hydrophobic interactions: G:I.21, G:F.32, G:F.32, G:A.36, G:W.39, M:L.9, M:L.12, M:I.13, P:L.57, P:A.111 BCR.70: 13 residues within 4Å: Chain F: F.15 Chain Q: F.17, W.20, V.35, I.38, L.42, T.43, V.47, I.50, A.54, L.102, L.106 Ligands: CLA.69 11 PLIP interactions: 1 interactions with chain F, 10 interactions with chain Q Hydrophobic interactions: F:F.15, Q:F.17, Q:W.20, Q:V.35, Q:I.38, Q:L.42, Q:L.42, Q:V.47, Q:I.50, Q:L.102, Q:L.106

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

LMG.20: 13 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: 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.23: 21 residues within 4Å: Chain A: Y.193, F.246, F.250, G.254, Y.258, Y.273, Q.277, T.452, V.456, F.463 Chain B: A.86, H.87, I.123, L.162, G.163, L.291 Chain E: L.65, Y.68, N.69 Ligands: CLA.2, CLA.8 14 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B, 3 interactions with chain E Hydrophobic interactions: A:F.246, A:F.250, A:T.452, A:V.456, A:F.463, B:L.162, B:L.291, E:L.65, E:Y.68, E:Y.68 Hydrogen bonds: A:Y.193, A:Q.277, B:H.87 Salt bridges: B:H.87 LMG.32: 13 residues within 4Å: Chain B: Y.67, G.70, C.71, N.72, F.73 Chain D: I.36, M.39, Q.40, R.44 Ligands: CLA.25, BCR.27, DGD.63, LHG.72 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:F.73, B:F.73 Hydrogen bonds: B:G.70, B:N.72, B:F.73, D:M.39, D:Q.40 LMG.39: 10 residues within 4Å: Chain G: D.23, V.27, V.30 Chain K: T.8, L.12 Chain P: H.62 Ligands: BCR.27, CLA.47, CLA.49, DGD.62 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain K Hydrophobic interactions: G:V.27, G:V.30, K:L.12 LMG.45: 11 residues within 4Å: Chain P: G.84, Y.85, G.86, D.95, P.98, V.101, S.102, L.105, H.106, S.109 Ligands: CLA.48 8 PLIP interactions: 8 interactions with chain P Hydrophobic interactions: P:Y.85, P:Y.85, P:P.98, P:V.101, P:L.105 Hydrogen bonds: P:G.86, P:D.95, P:F.170 LMG.71: 14 residues within 4Å: Chain F: K.5, Y.9 Chain P: V.202, S.204, F.206, D.209, W.211 Chain Q: F.93, W.97, Y.124 Ligands: CLA.50, CLA.51, DGD.61, CLA.69 6 PLIP interactions: 2 interactions with chain Q, 2 interactions with chain F, 2 interactions with chain P Hydrophobic interactions: Q:Y.124, P:W.211, P:W.211 Hydrogen bonds: Q:W.97, F:Y.9, F:Y.9

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

LHG.21: 14 residues within 4Å: Chain A: R.224, G.228 Chain B: F.15, D.19, W.32, E.131 Chain E: W.44, M.50, A.51, L.55 Chain L: A.87, I.90 Ligands: CLA.9, LHG.22 8 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A, 2 interactions with chain L, 2 interactions with chain B Hydrophobic interactions: E:W.44, E:A.51, E:L.55, L:A.87, L:I.90, B:F.15, B:W.32 Salt bridges: A:R.224 LHG.22: 14 residues within 4Å: Chain A: F.227, G.228, L.229, I.474 Chain B: R.23, L.36, E.131, R.134 Chain L: L.83 Ligands: CLA.8, CLA.9, LHG.21, CLA.26, LHG.42 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 interactions with chain L Hydrophobic interactions: B:L.36, A:L.229, L:L.83 Hydrogen bonds: B:R.23 LHG.24: 5 residues within 4Å: Chain A: W.185, A.204 Chain O: V.100, L.101 Ligands: CLA.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.185 LHG.29: 17 residues within 4Å: Chain A: Y.6, R.7, F.464, W.468 Chain B: Y.141, I.144, R.265, W.266, F.269, L.273, V.276, T.277, W.280 Chain O: S.49 Ligands: CLA.11, CLA.13, LHG.41 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.144, B:L.273, B:V.276, B:T.277, B:W.280, A:F.464 Hydrogen bonds: B:Y.141, B:R.265 Salt bridges: A:R.7 LHG.30: 23 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, L.23 Chain J: L.10, T.13, L.14, I.17, S.20, I.21 Ligands: PL9.28, PHO.34, LHG.41, CLA.67 18 PLIP interactions: 5 interactions with chain H, 7 interactions with chain B, 6 interactions with chain J Hydrophobic interactions: H:Y.19, H:W.20, H:L.23, B:F.257, B:F.257, B:F.261, J:L.10, J:L.14, J:I.17, J:I.17, J:I.21, J:I.21 Hydrogen bonds: H:N.14, H:T.16, B:S.262, B:S.262, B:N.263, B:N.263 LHG.31: 17 residues within 4Å: Chain B: E.219, N.220, A.229, N.230, T.231, F.232 Chain P: F.21, W.24, S.25, W.431, R.435 Chain Q: R.140, W.142, F.273, A.276, I.281 Ligands: CLA.53 10 PLIP interactions: 3 interactions with chain B, 4 interactions with chain P, 3 interactions with chain Q Hydrogen bonds: B:N.220, B:N.230, B:T.231, P:S.25, P:S.25 Hydrophobic interactions: P:W.24, P:W.431, Q:A.276, Q:I.281 Salt bridges: Q:R.140 LHG.40: 5 residues within 4Å: Chain G: S.44, F.45 Chain P: W.23 Ligands: BCR.38, SQD.64 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.44 LHG.41: 21 residues within 4Å: Chain A: W.5, Y.6 Chain B: W.266, F.270, L.273 Chain H: E.12, N.14, S.17, W.20, G.21, L.23, L.24, V.27 Chain I: I.17, F.21 Chain O: R.51 Ligands: CLA.11, PL9.28, LHG.29, LHG.30, CLA.33 12 PLIP interactions: 7 interactions with chain H, 1 interactions with chain A, 2 interactions with chain B, 2 interactions with chain I Hydrophobic interactions: H:L.23, H:L.24, H:V.27, B:F.270, B:L.273, I:I.17, I:F.21 Hydrogen bonds: H:E.12, H:N.14, H:S.17, H:S.17, A:Y.6 LHG.42: 17 residues within 4Å: Chain B: V.92, W.93, Q.98, G.99, F.101 Chain L: P.67, K.70, N.71, G.74, S.75, A.78, G.79, L.83 Ligands: CLA.8, LHG.22, CLA.26, BCR.27 7 PLIP interactions: 3 interactions with chain L, 4 interactions with chain B Hydrophobic interactions: L:L.83, B:V.92, B:W.93, B:F.101 Hydrogen bonds: L:N.71, B:Q.98 Salt bridges: L:K.70 LHG.72: 17 residues within 4Å: Chain D: I.25 Chain Q: F.211, M.214, L.218, H.252, F.255, I.259, F.260, Q.261, F.265, L.271, F.274 Ligands: LMG.32, PHO.35, CLA.49, DGD.63, CLA.68 4 PLIP interactions: 3 interactions with chain Q, 1 interactions with chain D Hydrophobic interactions: Q:F.260, Q:Q.261, D:I.25 Hydrogen bonds: Q:H.252

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: 27 residues within 4Å: Chain B: M.198, M.199, A.202, G.203, L.209, I.213, H.214, T.217, M.246, N.250, W.253, F.257, V.259, A.260, F.261, L.267, V.274, T.277 Chain H: V.27, V.30, L.31 Chain J: L.10 Chain Q: F.48 Ligands: LHG.30, CLA.33, PHO.34, LHG.41 16 PLIP interactions: 12 interactions with chain B, 1 interactions with chain Q, 2 interactions with chain H, 1 interactions with chain J Hydrophobic interactions: B:A.202, B:L.209, B:W.253, B:F.257, B:F.261, B:F.261, B:F.261, B:L.267, B:V.274, B:T.277, Q:F.48, H:V.30, H:L.31, J:L.10 Hydrogen bonds: B:T.217, B:F.261

2 x PHO: PHEOPHYTIN A(Non-covalent)

PHO.34: 25 residues within 4Å: Chain B: L.205, L.209, I.213, W.253, F.257 Chain Q: L.41, A.44, T.45, F.48, I.115, F.119, Y.126, E.130, A.146, Y.147, A.149, P.150, L.174, G.175, P.279, I.283 Ligands: PL9.28, LHG.30, CLA.33, CLA.67 15 PLIP interactions: 4 interactions with chain B, 11 interactions with chain Q Hydrophobic interactions: B:L.205, B:I.213, B:I.213, B:F.257, Q:L.41, Q:A.44, Q:F.48, Q:I.115, Q:F.119, Q:A.146, Q:Y.147, Q:A.149, Q:P.150, Q:L.174, Q:I.283 PHO.35: 27 residues within 4Å: Chain B: L.37, A.41, L.45, W.48, V.114, G.118, L.122, F.125, Q.129, N.142, A.145, F.146, A.148, P.149, F.153, G.174, V.175, P.275, L.279 Chain Q: F.206, S.209, L.210, M.214, L.258 Ligands: CLA.25, CLA.68, LHG.72 16 PLIP interactions: 1 interactions with chain Q, 15 interactions with chain B Hydrophobic interactions: Q:F.206, B:A.41, B:L.45, B:W.48, B:W.48, B:V.114, B:L.122, B:F.125, B:A.145, B:A.148, B:F.153, B:P.275, B:L.279 Hydrogen bonds: B:N.142 pi-Stacking: B:F.146, B:F.146

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

HEM.36: 17 residues within 4Å: Chain C: R.8, I.13, R.18, 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 R: L.48 16 PLIP interactions: 8 interactions with chain D, 8 interactions with chain C, Hydrophobic interactions: D:I.22, D:A.26, D:V.27, D:I.30, C:I.13, C:I.22, C:T.26, C:V.27, C:L.30 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: Q.24, V.28, L.35, F.38 Chain C: E.7 Chain D: F.15, T.16, V.17, A.21 Chain L: I.90, V.93, D.97 7 PLIP interactions: 2 interactions with chain L, 3 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: L:I.90, L:V.93, B:V.28, B:L.35, B:F.38, D:A.21 Hydrogen bonds: D:V.17

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

DGD.61: 27 residues within 4Å: Chain P: W.177, P.205, F.206, G.207, G.208, D.209, G.210, W.211, C.213, S.214, V.215, F.272, C.276, F.280, N.281, N.282, T.283, D.348, F.349, R.350, F.423, F.426 Chain Q: L.91, Y.124, S.155, I.163 Ligands: LMG.71 15 PLIP interactions: 2 interactions with chain Q, 13 interactions with chain P Hydrophobic interactions: Q:Y.124, Q:I.163, P:F.272, P:F.423, P:F.426 Hydrogen bonds: P:G.208, P:W.211, P:V.215, P:N.282, P:N.282, P:T.283, P:D.348, P:D.348, P:R.350, P:R.350 DGD.62: 9 residues within 4Å: Chain P: E.71, Q.72, G.73, S.394, V.408, W.413 Ligands: LMG.39, CLA.49, DGD.63 6 PLIP interactions: 6 interactions with chain P Hydrophobic interactions: P:W.413, P:W.413 Hydrogen bonds: P:E.71, P:S.394, P:S.394, P:V.408 DGD.63: 15 residues within 4Å: Chain B: N.72 Chain P: L.392, N.393 Chain Q: P.196, M.199, L.200, A.203, F.300, N.301, F.302 Ligands: LMG.32, CLA.49, DGD.62, CLA.68, LHG.72 7 PLIP interactions: 4 interactions with chain Q, 1 interactions with chain B, 2 interactions with chain P Hydrophobic interactions: Q:P.196, Q:A.203, Q:F.300, P:L.392 Hydrogen bonds: Q:N.301, B:N.72, P:N.393

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

SQD.64: 17 residues within 4Å: Chain B: N.230, F.232, R.233 Chain G: V.30, F.37 Chain P: A.22, W.24 Chain Q: N.267, S.270, F.273, F.274, A.277, W.278, I.281 Ligands: LHG.40, CLA.49, CLA.53 16 PLIP interactions: 3 interactions with chain G, 1 interactions with chain P, 10 interactions with chain Q, 2 interactions with chain B Hydrophobic interactions: G:V.30, G:F.37, G:F.37, P:W.24, Q:F.273, Q:F.274, Q:A.277, Q:W.278, Q:W.278, Q:W.278, Q:I.281 Hydrogen bonds: Q:N.267, Q:S.270, Q:S.270, B:N.230 Salt bridges: B:R.233

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

BCT.65: 9 residues within 4Å: Chain B: H.214, E.242, Y.244, H.268 Chain Q: H.215, V.219, N.247, H.272 Ligands: FE2.66 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:N.247

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

FE2.66: 5 residues within 4Å: Chain B: H.214, H.268 Chain Q: H.215, H.272 Ligands: BCT.65 4 PLIP interactions: 2 interactions with chain Q, 2 interactions with chain B Metal complexes: Q:H.215, Q:H.272, 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 Ycf12: K
Uncharacterized protein: L
Photosystem II reaction center protein Z: M
Thylakoid enriched factor 14 (TEF14): N
Photosystem II repair factor 1 (PRF1): O
Photosystem II CP43 reaction center protein: P
Photosystem II protein D1: Q
Photosystem II repair factor 2 (PRF2): R

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
G

O
3

P
C

Q
A

R
1

Membrane

We predict this structure to be a membrane protein.
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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 Ycf12

Uncharacterized protein

Photosystem II reaction center protein Z

Thylakoid enriched factor 14 (TEF14)

Photosystem II repair factor 1 (PRF1)

Photosystem II CP43 reaction center protein

Photosystem II protein D1

Photosystem II repair factor 2 (PRF2)

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