SMTL ID : 9iiu.1

Cryo-EM structure of an TEF30-associated intermediate PSII core complex from Chlamydomonas reinhardtii

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-mer

Ligands

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

FE2.1: 5 residues within 4Å: Chain A: H.206, H.263 Chain D: H.211, H.265 Ligands: BCT.54 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Metal complexes: A:H.206, A:H.263, D:H.211, D:H.265

35 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.2: 31 residues within 4Å: Chain A: F.110, V.114, Y.138, P.141, V.142, A.144, V.148, F.173, M.174, I.175, 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 Chain D: I.179, L.202, F.254 Ligands: CLA.3, PHO.4, CLA.52, CLA.55, LHG.59 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain D, Hydrophobic interactions: A:F.110, A:F.110, A:V.114, A:Y.138, A:A.144, A:F.173, A:F.177, A:Q.178, A:I.183, A:L.184, A:V.193, A:V.196, A:F.197, D:I.179, D:L.202, D:F.254 Metal complexes: A:H.189 CLA.3: 18 residues within 4Å: Chain A: M.190, V.193, A.194, F.197, G.198, L.201, W.269 Chain D: F.154, F.170, V.172, I.175, F.176, F.178, I.179 Ligands: CLA.2, PHO.53, CLA.55, DGD.65 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain A, Hydrophobic interactions: D:F.154, D:F.170, D:F.176, D:F.178, D:I.179, A:V.193, A:L.201, A:W.269 pi-Stacking: A:F.197 CLA.5: 23 residues within 4Å: Chain A: I.27, P.30, C.31, T.34, F.84, P.86, I.87, W.88, Q.104, L.105, C.108, H.109, L.112 Chain I: F.7, V.8, Y.9, V.11, V.12, T.13, F.15 Ligands: BCR.6, LMG.8, CLA.36 16 PLIP interactions: 10 interactions with chain A, 6 interactions with chain I, Hydrophobic interactions: A:I.27, A:P.30, A:F.84, A:P.86, A:I.87, A:W.88, A:L.105, I:F.7, I:V.8, I:V.11, I:V.12, I:T.13, I:F.15 Hydrogen bonds: A:I.87 Salt bridges: A:H.109 Metal complexes: A:H.109 CLA.10: 10 residues within 4Å: Chain B: W.184, G.185, A.186, F.189 Chain H: F.44, I.47, I.51, L.58 Ligands: CLA.11, BCR.64 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain H, Hydrophobic interactions: B:A.186, B:F.189, B:F.189, H:F.44, H:F.44, H:I.51, H:L.58 CLA.11: 28 residues within 4Å: Chain B: S.183, W.184, G.188, F.189, G.196, S.199, H.200, A.203, L.207, W.246, F.249, V.250, T.254 Chain D: V.151, L.155, I.156, L.159 Chain H: F.41, F.44, I.48, L.49, Y.52 Ligands: CLA.10, CLA.12, CLA.14, CLA.18, LMG.31, BCR.64 21 PLIP interactions: 10 interactions with chain B, 4 interactions with chain D, 7 interactions with chain H, Hydrophobic interactions: B:W.184, B:F.189, B:F.189, B:H.200, B:A.203, B:L.207, B:W.246, B:F.249, B:F.249, D:V.151, D:L.155, D:I.156, D:L.159, H:F.41, H:F.44, H:I.48, H:L.49, H:L.49, H:Y.52 Metal complexes: B:H.200 pi-Stacking: H:F.44 CLA.12: 26 residues within 4Å: Chain B: R.67, L.68, S.145, L.148, C.149, F.152, I.165, I.197, H.200, H.201, A.243, W.246, A.247, V.250, A.261 Chain H: I.38, F.41, L.45 Ligands: CLA.11, CLA.13, CLA.14, CLA.15, CLA.17, CLA.18, CLA.19, BCR.64 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain H, Hydrophobic interactions: B:L.68, B:L.148, B:L.148, B:F.152, B:F.152, B:A.243, B:W.246, B:W.246, B:A.247, B:V.250, B:V.250, H:F.41, H:F.41, H:L.45 Hydrogen bonds: B:R.67 Salt bridges: B:R.67 pi-Cation interactions: B:H.200 Metal complexes: B:H.201 CLA.13: 23 residues within 4Å: Chain B: W.32, F.60, F.64, R.67, L.147, L.148, V.244, A.247, A.248, V.251, F.450, H.454, F.457, A.458, F.461 Ligands: CLA.12, CLA.14, CLA.16, CLA.19, CLA.20, CLA.21, CLA.22, CLA.24 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:W.32, B:F.60, B:F.60, B:F.64, B:L.147, B:V.244, B:A.247, B:A.248, B:V.251, B:F.457, B:F.457, B:F.457, B:F.461, B:F.461 Salt bridges: B:R.67 Metal complexes: B:H.454 CLA.14: 24 residues within 4Å: Chain B: T.26, V.29, S.30, W.32, A.33, V.61, F.64, M.65, R.67, L.68, V.95, H.99, L.102, S.145, G.146, A.204, G.208 Ligands: CLA.11, CLA.12, CLA.13, CLA.15, CLA.19, CLA.21, CLA.24 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:T.26, B:V.29, B:W.32, B:A.33, B:L.68, B:V.95, B:L.102 Metal complexes: B:H.99 CLA.15: 20 residues within 4Å: Chain B: L.68, G.69, I.70, W.90, V.95, A.98, H.99, I.101, L.102, L.148, G.151, F.152, F.155, H.156, F.161, G.162, P.163 Ligands: CLA.12, CLA.14, BCR.28 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:L.68, B:I.70, B:A.98, B:L.102, B:L.148, B:L.148, B:F.152, B:F.155, B:F.161 Metal complexes: B:H.156 CLA.16: 23 residues within 4Å: Chain B: W.32, M.36, F.39, V.43, G.58, M.59, F.60, L.323, F.324, T.326, G.327, A.328, W.449, F.450 Chain D: F.193, M.278 Chain L: L.25, F.29 Ligands: CLA.13, CLA.22, BCR.27, LMG.29, LHG.30 11 PLIP interactions: 7 interactions with chain B, 3 interactions with chain L, 1 interactions with chain D, Hydrophobic interactions: B:F.60, B:F.60, B:L.323, B:F.324, B:T.326, B:W.449, L:L.25, L:F.29, L:F.29, D:F.193 pi-Stacking: B:F.60 CLA.17: 27 residues within 4Å: Chain B: L.228, T.235, S.238, S.239, A.242, W.246, F.462, H.465, I.466, G.469, T.472, I.473 Chain D: L.33, L.86, L.113, F.117, I.120, M.123, L.124 Chain H: L.46, L.49 Ligands: CLA.12, CLA.18, CLA.19, CLA.56, LHG.61, LHG.62 16 PLIP interactions: 8 interactions with chain D, 6 interactions with chain B, 2 interactions with chain H, Hydrophobic interactions: D:L.86, D:L.113, D:F.117, D:F.117, D:I.120, D:I.120, D:M.123, D:L.124, B:W.246, B:F.462, B:I.466, B:I.473, H:L.46, H:L.49 Hydrogen bonds: B:S.238 Metal complexes: B:H.465 CLA.18: 22 residues within 4Å: Chain B: F.138, L.142, L.207, A.211, F.214, H.215, P.220, L.228, M.230, W.246 Chain D: F.117 Chain H: T.30, L.33, M.34, F.37, I.38 Ligands: CLA.11, CLA.12, CLA.17, CLA.19, LHG.61, BCR.64 15 PLIP interactions: 3 interactions with chain H, 1 interactions with chain D, 11 interactions with chain B, Hydrophobic interactions: H:L.33, H:M.34, H:F.37, D:F.117, B:F.138, B:F.138, B:F.138, B:L.142, B:L.207, B:A.211, B:F.214, B:F.214, B:L.228, B:W.246 Metal complexes: B:H.215 CLA.19: 23 residues within 4Å: Chain B: L.18, H.22, L.134, P.135, I.137, F.138, H.141, L.142, S.145, M.230, I.233, V.236, S.239, S.240, A.243 Ligands: CLA.12, CLA.13, CLA.14, CLA.17, CLA.18, CLA.21, CLA.24, BCR.64 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:L.18, B:L.134, B:P.135, B:F.138, B:F.138, B:M.230, B:I.233, B:V.236 Hydrogen bonds: B:H.141 CLA.20: 22 residues within 4Å: Chain B: W.4, Y.5, R.6, V.7, H.8, T.9, L.237, I.241, L.460, F.461, F.463, G.464, W.467, H.468, R.471 Ligands: CLA.13, CLA.21, CLA.22, CLA.23, BCR.27, LHG.30, LHG.67 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:W.4, B:W.4, B:H.8, B:T.9, B:L.237, B:L.237, B:I.241, B:F.461, B:F.461, B:F.463, B:W.467 Salt bridges: B:H.8, B:R.471 pi-Stacking: B:W.467 Metal complexes: B:H.468 CLA.21: 22 residues within 4Å: Chain B: H.8, V.11, I.12, L.18, V.21, H.22, H.25, T.26, V.29, I.233, V.236, L.237, S.240, I.241, V.244 Ligands: CLA.13, CLA.14, CLA.19, CLA.20, CLA.22, CLA.23, CLA.24 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:H.8, B:I.12, B:V.21, B:V.21, B:V.29, B:I.233, B:V.236, B:L.237 Hydrogen bonds: B:S.240 Salt bridges: B:H.22 Metal complexes: B:H.22 CLA.22: 16 residues within 4Å: Chain B: H.8, H.25, L.28, V.29, W.32, L.460, F.461 Ligands: CLA.13, CLA.16, CLA.20, CLA.21, CLA.23, BCR.27, LMG.29, LHG.30, LHG.67 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:L.28, B:V.29, B:V.29, B:W.32, B:W.32, B:F.461 Salt bridges: B:H.8 Metal complexes: B:H.25 CLA.23: 17 residues within 4Å: Chain B: V.7, H.8, V.10, V.21, M.24, H.25, L.28, W.114 Chain L: Q.6, V.8 Chain M: F.18, L.22, K.25 Ligands: CLA.20, CLA.21, CLA.22, BCR.26 11 PLIP interactions: 3 interactions with chain M, 1 interactions with chain L, 7 interactions with chain B, Hydrophobic interactions: M:F.18, M:L.22, L:V.8, B:V.7, B:V.21, B:M.24, B:H.25, B:L.28, B:W.114 Hydrogen bonds: M:K.25 Metal complexes: B:H.8 CLA.24: 20 residues within 4Å: Chain B: I.19, H.22, L.23, T.26, L.102, L.121, F.122, L.132, I.137, I.140, H.141, L.144 Chain H: L.14, L.17, N.18 Ligands: CLA.13, CLA.14, CLA.19, CLA.21, CLA.25 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain H, Hydrophobic interactions: B:I.19, B:L.102, B:L.121, B:F.122, B:L.132, B:I.137, B:I.137, B:I.140, B:L.144, H:L.14, H:L.14, H:L.17 Metal complexes: B:H.141 CLA.25: 15 residues within 4Å: Chain B: I.19, L.23, L.106, A.109, W.112, H.113, L.119, L.121 Chain H: T.8, P.9, L.10, G.11, L.14 Ligands: CLA.24, BCR.28 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain H, Hydrophobic interactions: B:I.19, B:L.23, B:A.109, B:W.112, B:L.119, B:L.121, H:L.10, H:L.14 Metal complexes: B:H.113 CLA.32: 23 residues within 4Å: Chain C: T.71, L.72, L.145, G.148, A.149, L.152, I.201, M.207, I.210, H.214, I.217, E.221, A.255, M.259, I.262, M.266, A.273, Y.274 Ligands: CLA.33, CLA.34, CLA.37, CLA.38, BCR.46 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:L.145, C:L.152, C:I.201, C:I.217, C:A.255, C:M.259, C:I.262, C:A.273, C:Y.274 Hydrogen bonds: C:Y.274 Metal complexes: C:H.214 CLA.33: 23 residues within 4Å: Chain C: W.40, I.64, H.68, L.72, Y.74, L.151, I.256, M.259, A.263, S.267, Y.274, L.403, H.407, L.410, G.411, F.414 Ligands: CLA.32, CLA.34, CLA.35, CLA.40, CLA.41, CLA.43, LMG.50 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:W.40, C:I.64, C:L.72, C:L.151, C:L.151, C:I.256, C:A.263, C:L.410, C:F.414 Hydrogen bonds: C:Y.274 Salt bridges: C:H.68, C:H.407 pi-Stacking: C:W.40 Metal complexes: C:H.407 CLA.34: 20 residues within 4Å: Chain C: I.37, V.38, W.40, A.41, N.45, L.65, H.68, I.69, S.91, H.95, I.256, M.259 Ligands: CLA.32, CLA.33, CLA.38, CLA.40, CLA.41, CLA.43, CLA.44, LMU.51 5 PLIP interactions: 5 interactions with chain C, Hydrophobic interactions: C:I.37, C:V.38, C:A.41, C:I.256 Metal complexes: C:H.95 CLA.35: 26 residues within 4Å: Chain A: F.188, L.191, F.276 Chain C: W.40, M.44, F.47, Q.61, G.62, L.63, I.64, L.381, S.383, W.402, L.403, S.406, L.410 Chain K: P.17, V.21 Ligands: SQD.7, LHG.9, CLA.33, CLA.39, CLA.41, DGD.49, LMG.50, DGD.65 10 PLIP interactions: 4 interactions with chain A, 5 interactions with chain C, 1 interactions with chain K, Hydrophobic interactions: A:F.188, A:L.191, A:F.276, A:F.276, C:L.381, C:W.402, C:W.402, C:W.402, C:L.410, K:V.21 CLA.36: 23 residues within 4Å: Chain A: F.24, I.27, Y.115, M.118, W.122 Chain C: F.241, Y.251, G.254, A.255, V.258, F.415, H.418, L.419, A.422, R.426 Chain I: V.12, V.16, F.19, F.23 Ligands: CLA.5, LMG.8, CLA.38, BCR.46 18 PLIP interactions: 2 interactions with chain I, 9 interactions with chain C, 7 interactions with chain A, Hydrophobic interactions: I:V.12, I:V.16, C:F.241, C:Y.251, C:Y.251, C:F.415, C:L.419, C:A.422, A:F.24, A:F.24, A:F.24, A:I.27, A:Y.115, A:W.122, A:W.122 Hydrogen bonds: C:Y.251 Salt bridges: C:R.426 Metal complexes: C:H.418 CLA.37: 19 residues within 4Å: Chain C: L.138, L.142, W.200, L.220, E.221, G.224, W.227, H.228, T.231, T.232, P.233, W.234, W.236, A.237, F.241 Ligands: LMG.8, CLA.32, CLA.38, BCR.46 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:L.138, C:W.200, C:L.220, C:W.236, C:F.241 Hydrogen bonds: C:W.234 Metal complexes: C:H.228 CLA.38: 20 residues within 4Å: Chain C: M.134, T.135, L.138, H.141, L.142, L.145, E.221, F.241, W.243, Y.248, Y.251, S.252, A.255, M.259 Ligands: CLA.32, CLA.34, CLA.36, CLA.37, CLA.40, BCR.46 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:T.135, C:L.145, C:F.241, C:W.243, C:Y.248, C:Y.248, C:Y.251, C:Y.251, C:Y.251, C:A.255 CLA.39: 25 residues within 4Å: Chain A: F.188 Chain C: W.13, S.14, G.15, N.16, A.17, E.246, L.249, L.253, C.409, L.410, F.413, F.414, G.417, W.420, H.421, R.424 Chain K: F.28 Ligands: SQD.7, LHG.9, CLA.35, CLA.40, CLA.41, CLA.42, LMG.50 17 PLIP interactions: 15 interactions with chain C, 1 interactions with chain A, 1 interactions with chain K, Hydrophobic interactions: C:A.17, C:L.249, C:L.249, C:L.253, C:L.410, C:F.413, C:F.414, C:F.414, C:W.420, A:F.188, K:F.28 Hydrogen bonds: C:S.14, C:N.16, C:A.17 Salt bridges: C:R.424 pi-Stacking: C:W.420 Metal complexes: C:H.421 CLA.40: 25 residues within 4Å: Chain C: N.16, L.19, I.20, L.26, A.29, H.30, H.33, Y.126, W.128, I.137, H.141, L.145, G.245, E.246, Y.248, L.249, S.252, I.256 Ligands: CLA.33, CLA.34, CLA.38, CLA.39, CLA.41, CLA.42, CLA.43 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:N.16, C:L.19, C:A.29, C:H.33, C:W.128, C:I.137, C:Y.248, C:L.249, C:L.249 Hydrogen bonds: C:S.252 Metal complexes: C:H.30 CLA.41: 19 residues within 4Å: Chain C: N.16, H.33, L.36, I.37, W.40, F.413, F.414 Chain K: P.20, V.21, I.24 Ligands: SQD.7, LHG.9, CLA.33, CLA.34, CLA.35, CLA.39, CLA.40, CLA.42, LMG.50 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain K, Hydrophobic interactions: C:L.36, C:I.37, C:W.40, C:W.40, C:F.413, C:F.414, K:P.20, K:P.20, K:V.21, K:I.24 Hydrogen bonds: C:N.16 Metal complexes: C:H.33 CLA.42: 32 residues within 4Å: Chain C: G.1, G.2, R.3, W.12, G.15, N.16, R.18, L.19, K.25, A.29, A.32, L.36, V.107, S.110, L.111 Chain K: F.23, L.26, A.27, W.30, Q.31 Chain O: V.21, V.22, L.25, N.31, L.32 Chain Q: V.23, P.24, A.28 Ligands: CLA.39, CLA.40, CLA.41, BCR.47 20 PLIP interactions: 7 interactions with chain K, 8 interactions with chain C, 2 interactions with chain O, 3 interactions with chain Q, Hydrophobic interactions: K:F.23, K:L.26, K:A.27, K:W.30, K:W.30, K:Q.31, C:K.25, C:A.32, C:L.36, C:V.107, C:L.111, O:V.21, O:V.22, Q:V.23, Q:P.24, Q:A.28 pi-Stacking: K:W.30 Hydrogen bonds: C:G.1, C:R.18 Salt bridges: C:K.25 CLA.43: 20 residues within 4Å: Chain C: L.27, H.30, V.31, A.34, L.102, F.123, F.124, Y.126, K.133, I.137, Y.140, H.141, M.144, G.148, L.151 Ligands: CLA.33, CLA.34, CLA.40, CLA.44, BCR.45 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:L.27, C:L.27, C:H.30, C:F.124, C:Y.126, C:Y.126, C:I.137, C:I.137, C:Y.140 Metal complexes: C:H.141 CLA.44: 14 residues within 4Å: Chain C: L.27, V.31, V.101, F.104, G.105, Y.108, H.109, L.117, Y.121, F.124, M.144 Ligands: CLA.34, CLA.43, BCR.45 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:L.27, C:L.27, C:V.31, C:V.31, C:V.101, C:F.104, C:Y.108, C:L.117, C:F.124 Metal complexes: C:H.109 CLA.52: 24 residues within 4Å: Chain A: F.39, I.40, F.110, V.148, F.149, M.163, I.167, T.170, F.171, F.173, M.174 Chain D: M.195, V.198, A.199, L.202, G.203, L.206 Chain N: L.14 Ligands: CLA.2, PHO.4, CLA.55, PL9.58, LHG.59, LHG.67 9 PLIP interactions: 7 interactions with chain A, 1 interactions with chain N, 1 interactions with chain D, Hydrophobic interactions: A:F.39, A:I.40, A:F.110, A:V.148, A:F.149, A:F.171, A:F.173, N:L.14, D:L.206 CLA.55: 28 residues within 4Å: Chain A: M.174, F.197 Chain D: L.42, W.45, L.119, F.143, P.146, V.149, S.152, V.153, F.178, I.179, F.182, Q.183, W.188, T.189, H.194, G.197, V.198, V.201, L.202, S.279, A.280, V.283 Ligands: CLA.2, CLA.3, CLA.52, PHO.53 19 PLIP interactions: 1 interactions with chain A, 18 interactions with chain D, Hydrophobic interactions: A:F.197, D:L.42, D:W.45, D:W.45, D:L.119, D:F.143, D:P.146, D:V.149, D:F.178, D:I.179, D:F.182, D:Q.183, D:T.189, D:V.198, D:V.201, D:V.201, D:L.202 pi-Stacking: D:W.188 Metal complexes: D:H.194 CLA.56: 26 residues within 4Å: Chain D: L.32, L.33, P.36, C.37, F.40, L.86, L.87, F.88, V.89, W.90, W.101, G.106, A.109, F.110, L.113, H.114, F.117 Chain H: L.39, L.46 Chain P: L.10, L.13, G.16, L.20 Ligands: CLA.17, LHG.62, BCR.64 19 PLIP interactions: 13 interactions with chain D, 2 interactions with chain H, 4 interactions with chain P, Hydrophobic interactions: D:L.33, D:P.36, D:F.40, D:F.40, D:F.88, D:F.88, D:V.89, D:W.90, D:L.113, D:F.117, H:L.39, H:L.46, P:L.10, P:L.13, P:L.13, P:L.20 Hydrogen bonds: D:V.89 pi-Stacking: D:F.110 Metal complexes: D:H.114

2 x PHO: PHEOPHYTIN A(Non-covalent)

PHO.4: 29 residues within 4Å: Chain A: L.32, A.35, T.36, F.39, F.110, Y.117, E.121, A.137, Y.138, A.140, P.141, F.149, L.165, G.166, T.170, P.270, V.271, I.274 Chain D: L.202, A.205, L.206, A.209, I.210, W.250, F.254 Ligands: CLA.2, CLA.52, PL9.58, LHG.59 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:L.32, A:A.35, A:F.39, A:F.110, A:Y.117, A:A.137, A:A.140, A:P.141, A:F.149, A:L.165, A:L.165, A:P.270, A:I.274, A:I.274, D:L.202, D:A.205, D:A.209, D:F.254 Hydrogen bonds: A:Y.138 PHO.53: 30 residues within 4Å: Chain A: F.197, S.200, L.201, M.205, L.249, I.250 Chain D: L.34, A.38, L.42, W.45, V.111, G.115, G.118, L.119, F.122, Q.126, N.139, A.142, F.143, A.145, P.146, F.150, F.170, G.171, V.172, I.175, P.272, L.276 Ligands: CLA.3, CLA.55 20 PLIP interactions: 19 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:A.38, D:L.42, D:W.45, D:W.45, D:V.111, D:L.119, D:F.122, D:F.122, D:A.142, D:A.145, D:F.150, D:F.170, D:F.170, D:V.172, D:I.175, D:P.272, D:L.276, A:F.197 Hydrogen bonds: D:N.139 pi-Stacking: D:F.143

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

BCR.6: 15 residues within 4Å: Chain A: F.8, W.11, I.12, I.29, L.33, T.34, S.37, V.38, I.41, A.45, I.87, W.96, L.97 Chain I: F.15 Ligands: CLA.5 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: A:F.8, A:W.11, A:I.12, A:I.29, A:V.38, A:I.41, A:I.87, A:W.96, A:L.97, A:L.97, I:F.15 BCR.26: 10 residues within 4Å: Chain B: M.24, F.107, S.110, V.111, W.114 Chain M: A.7 Ligands: CLA.23, BCR.27, LMG.29, LHG.67 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain M Hydrophobic interactions: B:F.107, B:V.111, B:W.114, M:A.7 BCR.27: 12 residues within 4Å: Chain B: L.28, G.31, W.32, I.100, S.103, G.104, A.105 Ligands: CLA.16, CLA.20, CLA.22, BCR.26, LMG.29 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.28, B:W.32, B:I.100 BCR.28: 9 residues within 4Å: Chain B: L.102, A.105, L.106, L.108, V.111, T.115, Y.116 Ligands: CLA.15, CLA.25 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.105, B:L.106, B:L.108, B:V.111, B:T.115 BCR.45: 12 residues within 4Å: Chain C: V.93, L.94, I.97, S.98, V.101, L.102, F.124 Chain Q: F.52, G.55, N.58 Ligands: CLA.43, CLA.44 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.93, C:I.97, C:V.101, C:V.101, C:L.102, C:F.124, C:F.124 BCR.46: 19 residues within 4Å: Chain C: I.186, F.187, Y.189, L.190, I.201, V.204, D.209, I.210, G.213, I.217, A.240, F.241 Chain I: I.20, F.23, L.24 Ligands: CLA.32, CLA.36, CLA.37, CLA.38 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain I Hydrophobic interactions: C:I.186, C:I.186, C:F.187, C:Y.189, C:Y.189, C:L.190, C:L.190, C:I.201, C:V.204, C:I.217, C:F.241, I:I.20, I:F.23, I:L.24 BCR.47: 23 residues within 4Å: Chain C: A.32, G.35, L.36, F.39, L.46, V.93, L.96, S.99, A.100, G.103, S.110, L.111 Chain K: F.9, I.12, V.13, F.23, A.27, W.30 Chain Q: L.9, I.13, S.16 Ligands: CLA.42, BCR.66 17 PLIP interactions: 9 interactions with chain C, 7 interactions with chain K, 1 interactions with chain Q Hydrophobic interactions: C:A.32, C:L.36, C:F.39, C:F.39, C:L.46, C:V.93, C:V.93, C:A.100, C:L.111, K:I.12, K:V.13, K:F.23, K:F.23, K:F.23, K:A.27, K:W.30, Q:L.9 BCR.57: 13 residues within 4Å: Chain D: Y.39, F.40, G.43, L.46, T.47, F.98, F.110 Chain F: P.15, T.16, F.19, I.23 Chain J: L.18 Ligands: LMG.60 13 PLIP interactions: 6 interactions with chain D, 6 interactions with chain F, 1 interactions with chain J Hydrophobic interactions: D:Y.39, D:F.40, D:L.46, D:L.46, D:F.98, D:F.110, F:P.15, F:T.16, F:F.19, F:F.19, F:F.19, F:I.23, J:L.18 BCR.64: 15 residues within 4Å: Chain H: F.37, I.38, L.40, F.41, F.44, I.47 Chain P: A.1, V.2, L.6 Ligands: CLA.10, CLA.11, CLA.12, CLA.18, CLA.19, CLA.56 8 PLIP interactions: 3 interactions with chain P, 5 interactions with chain H Hydrophobic interactions: P:V.2, P:L.6, P:L.6, H:F.37, H:I.38, H:F.41, H:F.44, H:I.47 BCR.66: 23 residues within 4Å: Chain J: G.7, T.8, G.11, T.12 Chain K: I.12, L.16, I.19, F.22, F.23, L.25, L.26, F.28, V.29, F.36 Chain O: V.14, V.15, A.17, G.18, P.19 Chain Q: I.13, S.16, F.17 Ligands: BCR.47 18 PLIP interactions: 11 interactions with chain K, 4 interactions with chain O, 2 interactions with chain Q, 1 interactions with chain J Hydrophobic interactions: K:I.12, K:L.16, K:I.19, K:F.22, K:F.23, K:F.23, K:L.25, K:L.26, K:F.28, K:V.29, K:F.36, O:V.14, O:V.15, O:A.17, O:P.19, Q:I.13, Q:F.17, J:T.8

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

SQD.7: 23 residues within 4Å: Chain A: L.191, G.195, R.260, S.261, F.264, F.265, A.268, W.269, I.272, G.273 Chain C: Q.5, W.12, W.13 Chain D: E.216 Chain K: I.24, L.25, F.28 Ligands: LHG.9, CLA.35, CLA.39, CLA.41, DGD.49, LMG.50 16 PLIP interactions: 4 interactions with chain K, 3 interactions with chain C, 8 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: K:I.24, K:L.25, K:F.28, K:F.28, C:W.12, C:W.13, A:F.264, A:A.268, A:W.269, A:W.269, A:W.269, A:I.272 Hydrogen bonds: C:Q.5, A:R.260, A:S.261, D:E.216

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

LMG.8: 22 residues within 4Å: Chain A: F.84, W.88, E.89, C.108, L.111, L.112, Y.115, L.150 Chain C: L.190, V.191, S.193, P.194, F.195, D.198, W.200, F.261 Chain I: K.5, Y.9 Ligands: CLA.5, CLA.36, CLA.37, DGD.48 14 PLIP interactions: 7 interactions with chain A, 3 interactions with chain I, 4 interactions with chain C Hydrophobic interactions: A:F.84, A:L.111, A:L.111, A:L.112, A:L.150, C:P.194, C:F.195, C:F.195, C:F.261 Hydrogen bonds: A:W.88, A:E.89, I:K.5, I:K.5, I:Y.9 LMG.29: 18 residues within 4Å: Chain B: T.326, G.327, A.328, S.331, F.452, G.453, C.456, F.457, L.460 Chain D: I.281 Chain L: I.33 Chain M: Y.3, G.4, A.7 Ligands: CLA.16, CLA.22, BCR.26, BCR.27 12 PLIP interactions: 9 interactions with chain B, 1 interactions with chain D, 1 interactions with chain L, 1 interactions with chain M Hydrophobic interactions: B:F.452, B:F.452, B:F.457, B:L.460, D:I.281, L:I.33, M:A.7 Hydrogen bonds: B:T.326, B:T.326, B:A.328, B:S.331, B:S.331 LMG.31: 25 residues within 4Å: Chain B: Y.192, F.249, W.256, Y.257, Y.272, Q.276, T.451, V.455, F.462 Chain D: A.83, H.84, L.86, L.113, F.117, I.120, V.151, L.155, I.156, L.159, G.160, L.288 Chain H: L.49, Y.52, N.53 Ligands: CLA.11 19 PLIP interactions: 8 interactions with chain B, 10 interactions with chain D, 1 interactions with chain H Hydrophobic interactions: B:F.249, B:Y.257, B:T.451, B:V.455, B:F.462, B:F.462, D:L.86, D:L.113, D:F.117, D:I.120, D:V.151, D:L.155, D:L.159, D:L.288, H:Y.52 Hydrogen bonds: B:Y.192, B:Q.276, D:H.84 Salt bridges: D:H.84 LMG.50: 16 residues within 4Å: Chain C: F.47, H.51, L.410 Chain J: I.15 Chain K: D.14, V.15, V.18, V.21, F.22 Chain O: T.7 Ligands: SQD.7, CLA.33, CLA.35, CLA.39, CLA.41, DGD.49 8 PLIP interactions: 4 interactions with chain K, 1 interactions with chain J, 2 interactions with chain C, 1 interactions with chain O Hydrophobic interactions: K:V.15, K:V.18, K:V.21, K:F.22, J:I.15, C:L.410, O:T.7 Salt bridges: C:H.51 LMG.60: 14 residues within 4Å: Chain D: Y.64, G.67, C.68, N.69, F.70 Chain F: M.26, Q.27 Chain J: F.21, G.24, S.25, L.29, G.30 Ligands: BCR.57, DGD.65 8 PLIP interactions: 2 interactions with chain F, 3 interactions with chain D, 3 interactions with chain J Hydrogen bonds: F:M.26, F:Q.27, D:F.70, J:G.24, J:G.30 Hydrophobic interactions: D:Y.64, D:F.70, J:F.21

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

LHG.9: 16 residues within 4Å: Chain A: R.131, W.133, F.264, A.267, W.275, F.276 Chain C: G.9, W.13, S.14, W.420 Chain D: E.216, N.217 Ligands: SQD.7, CLA.35, CLA.39, CLA.41 11 PLIP interactions: 4 interactions with chain C, 6 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: C:W.13, C:W.420, C:W.420, A:F.264, A:F.264, A:W.275, A:W.275, A:F.276 Hydrogen bonds: C:S.14, D:N.217 Salt bridges: A:R.131 LHG.30: 20 residues within 4Å: Chain B: Y.5, R.6, L.460, F.463, W.467 Chain D: Y.138, I.141, M.196, R.262, F.266, L.270, V.273, T.274, W.277, M.278 Ligands: CLA.16, CLA.20, CLA.22, PL9.58, LHG.67 12 PLIP interactions: 4 interactions with chain B, 8 interactions with chain D Hydrophobic interactions: B:L.460, B:F.463, D:L.270, D:L.270, D:V.273, D:T.274, D:W.277 Hydrogen bonds: B:Y.5, D:Y.138, D:R.262, D:R.262 Salt bridges: B:R.6 LHG.59: 24 residues within 4Å: Chain A: M.28, Y.117 Chain D: I.253, F.254, V.256, A.257, F.258, S.259, N.260, W.263 Chain L: T.13, Y.16, W.17, L.20 Chain N: L.10, T.13, I.17, S.20, I.21 Ligands: CLA.2, PHO.4, CLA.52, PL9.58, LHG.67 16 PLIP interactions: 9 interactions with chain D, 5 interactions with chain L, 1 interactions with chain N, 1 interactions with chain A Hydrophobic interactions: D:F.254, D:F.254, D:F.254, D:V.256, D:F.258, L:Y.16, L:W.17, L:W.17, L:L.20, N:L.10, A:Y.117 Hydrogen bonds: D:S.259, D:S.259, D:N.260, D:N.260, L:N.11 LHG.61: 15 residues within 4Å: Chain B: R.223, G.227, L.228 Chain D: F.12, D.16, R.20, W.29, S.30, L.32, L.33, L.124, E.128, R.131 Ligands: CLA.17, CLA.18 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain D Hydrophobic interactions: B:L.228, D:F.12, D:W.29, D:W.29, D:W.29, D:L.32, D:L.33, D:L.124, D:R.131 Hydrogen bonds: B:R.223, B:R.223 LHG.62: 14 residues within 4Å: Chain D: V.89, W.90, Q.95, G.96, F.98 Chain E: V.39 Chain P: N.8, G.11, S.12, A.15, G.16, L.20 Ligands: CLA.17, CLA.56 7 PLIP interactions: 3 interactions with chain P, 4 interactions with chain D Hydrophobic interactions: P:A.15, D:W.90, D:W.90, D:F.98, D:F.98 Hydrogen bonds: P:N.8, P:G.11 LHG.67: 21 residues within 4Å: Chain B: P.3, W.4, Y.5 Chain D: W.263, F.266, L.270 Chain L: E.9, S.14, W.17, G.18, L.21, V.24 Chain M: I.14, F.18 Ligands: CLA.20, CLA.22, BCR.26, LHG.30, CLA.52, PL9.58, LHG.59 11 PLIP interactions: 8 interactions with chain L, 2 interactions with chain M, 1 interactions with chain D Hydrophobic interactions: L:W.17, L:L.21, L:V.24, L:V.24, M:I.14, M:F.18, D:L.270 Hydrogen bonds: L:E.9, L:E.9, L:S.14, L:G.18

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

DGD.48: 28 residues within 4Å: Chain A: L.82, Y.115, V.142, S.146, L.150, I.154 Chain C: W.166, P.194, F.195, G.196, G.197, G.199, W.200, C.202, S.203, V.204, F.261, C.265, F.269, N.270, N.271, D.337, F.338, R.339, F.408, F.412, F.415 Ligands: LMG.8 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:P.194, C:F.195, C:W.200, C:F.261, C:F.408, C:F.412, C:F.412, C:F.415, C:F.415, A:Y.115, A:V.142, A:I.154 Hydrogen bonds: C:G.197, C:V.204, C:N.271, C:D.337, C:R.339 DGD.49: 22 residues within 4Å: Chain A: H.186, F.188, T.283, L.288 Chain C: E.60, Q.61, G.62, L.381, N.382, S.383, N.395, F.396, V.397, W.402, C.405, S.406 Chain J: F.22, Y.26 Ligands: SQD.7, CLA.35, LMG.50, DGD.65 14 PLIP interactions: 10 interactions with chain C, 2 interactions with chain J, 2 interactions with chain A Hydrophobic interactions: C:L.381, C:W.402, C:W.402, J:F.22, J:F.22, A:T.283, A:L.288 Hydrogen bonds: C:E.60, C:N.382, C:S.383, C:N.395, C:V.397, C:V.397, C:W.402 DGD.65: 25 residues within 4Å: Chain A: P.187, M.190, L.191, A.194, F.291, N.292, F.293, S.296 Chain C: L.381, N.382, V.384, N.392, V.394, N.395 Chain D: N.69, L.71 Chain J: F.22, S.25, Y.26, G.30, S.32 Ligands: CLA.3, CLA.35, DGD.49, LMG.60 18 PLIP interactions: 8 interactions with chain A, 4 interactions with chain C, 2 interactions with chain D, 4 interactions with chain J Hydrophobic interactions: A:P.187, A:P.187, A:M.190, A:L.191, A:A.194, A:F.291, A:F.291, A:F.291, D:L.71, J:F.22 Hydrogen bonds: C:N.382, C:N.392, C:N.392, C:V.394, D:N.69, J:S.25, J:Y.26, J:G.30

1 x LMU: DODECYL-ALPHA-D-MALTOSIDE(Non-covalent)

LMU.51: 10 residues within 4Å: Chain C: V.38, Y.74, D.84, P.87, V.90, S.91, L.94, H.95, S.98 Ligands: CLA.34 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.38, C:Y.74, C:L.94

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

BCT.54: 8 residues within 4Å: Chain A: H.206, V.210, H.263 Chain D: E.239, Y.241, K.261, H.265 Ligands: FE2.1 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.241

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)

PL9.58: 37 residues within 4Å: Chain A: F.39, F.43, I.68, I.167 Chain D: M.195, M.196, A.199, G.200, G.203, L.206, I.210, H.211, T.214, V.215, Y.241, M.243, A.246, N.247, W.250, F.254, V.256, A.257, F.258, L.264, F.267, V.271, T.274, G.275 Chain L: L.21, V.24, L.28 Chain N: L.10 Ligands: PHO.4, LHG.30, CLA.52, LHG.59, LHG.67 23 PLIP interactions: 15 interactions with chain D, 2 interactions with chain L, 4 interactions with chain A, 2 interactions with chain N Hydrophobic interactions: D:M.196, D:L.206, D:I.210, D:Y.241, D:F.254, D:F.258, D:F.258, D:F.258, D:L.264, D:F.267, D:V.271, D:T.274, L:L.21, L:L.28, A:F.39, A:F.43, A:F.43, A:I.68, N:L.10, N:L.10 Hydrogen bonds: D:H.211, D:T.214, D:F.258

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

HEM.63: 15 residues within 4Å: Chain E: I.6, Y.12, H.16, T.19, V.20, L.23 Chain F: I.1, T.3, R.5, W.6, I.9, H.10, A.13, V.14, I.17 15 PLIP interactions: 7 interactions with chain E, 8 interactions with chain F, Hydrophobic interactions: E:I.6, E:Y.12, E:T.19, E:V.20, E:L.23, F:I.1, F:I.9, F:A.13 pi-Stacking: E:Y.12, F:W.6, F:H.10 Metal complexes: E:H.16 Hydrogen bonds: F:I.1, F:T.3 Salt bridges: F:R.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., TEF30 fulfills versatile functions in the photosystem II repair process. To Be Published

Release Date

2025-05-14

Peptides

Photosystem II protein D1: A
Photosystem II CP47 reaction center protein: B
Photosystem II CP43 reaction center protein: C
Photosystem II D2 protein: D
Cytochrome b559 subunit alpha: E
Cytochrome b559 subunit beta: F
PDZ domain-containing protein: G
Photosystem II reaction center protein H: H
Photosystem II reaction center protein I: I
Photosystem II reaction center protein J: J
Photosystem II reaction center protein K: K
Photosystem II reaction center protein L: L
Photosystem II reaction center protein M: M
Photosystem II reaction center protein T: N
Photosystem II reaction center protein Psb30: O
Chloroplast photosystem II subunit X: P
Photosystem II reaction center protein Z: Q

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
T

O
V

P
X

Q
Z

Membrane

We predict this structure to be a membrane protein.
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Photosystem II protein D1

Photosystem II CP47 reaction center protein

Photosystem II CP43 reaction center protein

Photosystem II D2 protein

Cytochrome b559 subunit alpha

Cytochrome b559 subunit beta

PDZ domain-containing protein

Photosystem II reaction center protein H

Photosystem II reaction center protein I

Photosystem II reaction center protein J

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

Chloroplast photosystem II subunit X

Photosystem II reaction center protein Z

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