SMTL ID : 8r2i.1

Cryo-EM Structure of native Photosystem II assembly intermediate from Chlamydomonas reinhardtii

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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.205, H.262 Chain D: H.212, H.266 Ligands: BCT.50 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Metal complexes: A:H.205, A:H.262, D:H.212, D:H.266

35 x CLA: CHLOROPHYLL A(Covalent)(Non-covalent)

CLA.2: 29 residues within 4Å: Chain A: F.109, Y.137, P.140, A.143, A.144, V.147, F.172, M.173, I.174, F.176, Q.177, I.182, L.183, H.188, G.191, V.192, V.195, F.196, I.273, T.276, A.277, L.280 Chain D: I.180, L.203, F.255 Ligands: CLA.3, PHO.4, CLA.48, CLA.51 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain D, Hydrophobic interactions: A:F.109, A:P.140, A:A.144, A:F.172, A:F.176, A:Q.177, A:I.182, A:I.182, A:L.183, A:V.192, A:V.192, A:V.195, A:F.196, A:I.273, D:I.180, D:I.180, D:F.255 pi-Stacking: A:H.188 pi-Cation interactions: A:H.188 Metal complexes: A:H.188 CLA.3: 15 residues within 4Å: Chain A: M.189, V.192, A.193, F.196, G.197, L.200 Chain D: F.155, V.173, I.176, F.177, F.179, I.180 Ligands: CLA.2, PHO.49, CLA.51 10 PLIP interactions: 6 interactions with chain D, 3 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: D:F.155, D:I.176, D:F.177, D:F.179, D:I.180, D:I.180, A:V.192, A:A.193, A:L.200 Metal complexes: H2O.1 CLA.5: 22 residues within 4Å: Chain A: I.26, P.29, C.30, T.33, F.83, P.85, I.86, W.87, Q.103, L.104, C.107, H.108, L.111 Chain H: F.7, V.8, Y.9, V.12, T.13, F.15 Ligands: BCR.6, BOG.7, CLA.34 14 PLIP interactions: 4 interactions with chain H, 10 interactions with chain A, Hydrophobic interactions: H:F.7, H:V.12, H:T.13, H:F.15, A:I.26, A:F.83, A:P.85, A:I.86, A:W.87, A:L.104 Hydrogen bonds: A:I.86 Salt bridges: A:H.108 pi-Stacking: A:H.108 Metal complexes: A:H.108 CLA.8: 7 residues within 4Å: Chain B: W.184, G.185, F.189 Chain G: F.42, I.45 Ligands: CLA.9, BCR.57 5 PLIP interactions: 3 interactions with chain G, 1 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: G:F.42, G:F.42, G:I.45, B:F.189 Metal complexes: H2O.1 CLA.9: 24 residues within 4Å: Chain B: G.188, F.189, P.191, G.196, S.199, H.200, A.203, L.207, W.246, F.249, V.250, T.254 Chain D: L.156, I.157, L.160 Chain G: F.39, F.42, I.46, L.47, Y.50 Ligands: CLA.8, CLA.10, BCR.57, LMG.58 22 PLIP interactions: 5 interactions with chain G, 14 interactions with chain B, 3 interactions with chain D, Hydrophobic interactions: G:F.39, G:F.39, G:F.42, G:L.47, B:F.189, B:F.189, B:A.203, B:L.207, B:W.246, B:W.246, B:W.246, B:W.246, B:F.249, B:F.249, B:V.250, B:V.250, D:L.156, D:I.157, D:L.160 pi-Stacking: G:F.42 Salt bridges: B:H.200 Metal complexes: B:H.200 CLA.10: 23 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, W.246, A.247, V.250, V.251, A.261 Chain G: F.39, L.43 Ligands: CLA.9, CLA.11, CLA.12, CLA.13, CLA.16, CLA.17 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain G, Hydrophobic interactions: B:L.68, B:L.148, B:L.148, B:F.152, B:F.152, B:I.197, B:A.247, B:V.250, G:F.39, G:F.39, G:L.43 Salt bridges: B:R.67 pi-Stacking: B:H.201 Metal complexes: B:H.201 CLA.11: 24 residues within 4Å: Chain B: W.32, F.60, F.64, R.67, L.144, L.148, V.244, A.247, A.248, V.251, M.255, F.450, H.454, F.457, A.458, F.461 Ligands: CLA.10, CLA.12, CLA.14, CLA.17, CLA.18, CLA.19, CLA.20, CLA.22 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:W.32, B:F.60, B:F.64, B:F.64, B:L.144, B:L.148, B:A.247, B:V.251, B:F.457, B:F.457, B:F.457, B:F.457, B:F.461, B:F.461 Salt bridges: B:R.67 pi-Stacking: B:F.450, B:F.450, B:H.454 Metal complexes: B:H.454 CLA.12: 23 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.10, CLA.11, CLA.13, CLA.17, CLA.19, LMT.28 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:T.26, B:V.29, B:W.32, B:A.33, B:F.64, B:L.68, B:V.95, B:L.102 Hydrogen bonds: B:M.65 Metal complexes: B:H.99 CLA.13: 17 residues within 4Å: Chain B: L.68, G.69, I.70, W.90, V.95, A.98, H.99, G.151, F.152, F.155, H.156, F.161, P.163 Ligands: CLA.10, CLA.12, BCR.25, LMT.28 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:L.68, B:L.68, B:I.70, B:I.70, B:W.90, B:W.90, B:W.90, B:A.98, B:F.152, B:F.155, B:F.161, B:F.161 Metal complexes: B:H.156 CLA.14: 17 residues within 4Å: Chain B: W.32, M.36, F.39, G.58, M.59, F.60, L.323, T.326, G.327, W.449, F.450, F.457 Chain D: F.194 Ligands: CLA.11, CLA.20, BCR.24, LMG.26 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: B:F.39, B:F.60, B:T.326, B:W.449, B:W.449, B:F.457, D:F.194 pi-Stacking: B:F.60 CLA.15: 20 residues within 4Å: Chain B: L.228, S.238, S.239, A.242, F.245, W.246, F.462, H.465, I.466, G.469, T.472 Chain D: F.118, I.121, M.124, L.125 Chain G: L.44 Ligands: CLA.16, CLA.17, CLA.52, LMG.58 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain D, Hydrophobic interactions: B:A.242, B:F.245, B:W.246, B:W.246, B:F.462, B:I.466, D:F.118, D:I.121, D:L.125 pi-Cation interactions: B:H.465 Metal complexes: B:H.465 CLA.16: 15 residues within 4Å: Chain B: F.138, L.207, A.211, F.214, H.215, P.220, L.224 Chain G: T.28, L.31, M.32, F.35 Ligands: CLA.10, CLA.15, CLA.17, BCR.57 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain G, Hydrophobic interactions: B:F.138, B:F.138, B:L.207, B:A.211, B:F.214, B:F.214, B:L.224, G:L.31, G:M.32, G:F.35 pi-Stacking: B:H.215, B:H.215 Metal complexes: B:H.215 Hydrogen bonds: G:T.28 CLA.17: 21 residues within 4Å: Chain B: L.18, H.22, L.134, I.137, F.138, H.141, L.142, S.145, M.230, I.233, V.236, S.239, S.240 Ligands: CLA.10, CLA.11, CLA.12, CLA.15, CLA.16, CLA.19, CLA.22, BCR.57 10 PLIP interactions: 9 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:L.18, B:L.134, B:L.134, B:I.137, B:F.138, B:H.141, B:M.230, B:I.233, B:V.236 Metal complexes: H2O.1 CLA.18: 21 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.11, CLA.19, CLA.20, CLA.21, BCR.24, LHG.29 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:W.4, B:L.237, B:L.237, B:I.241, B:F.461, B:F.463 Hydrogen bonds: B:V.7, B:H.8 Salt bridges: B:H.8, B:R.471 pi-Stacking: B:W.467 pi-Cation interactions: B:H.468 Metal complexes: B:H.468 CLA.19: 21 residues within 4Å: Chain B: H.8, V.11, I.12, L.18, V.21, H.22, H.25, T.26, I.233, E.234, V.236, L.237, S.240, V.244 Ligands: CLA.11, CLA.12, CLA.17, CLA.18, CLA.20, CLA.21, CLA.22 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:V.11, B:I.12, B:L.18, B:V.21, B:V.21, B:I.233, B:V.236, B:L.237, B:L.237, B:L.237, B:V.244 Hydrogen bonds: B:S.240 Salt bridges: B:H.22 pi-Stacking: B:H.22, B:H.22 Metal complexes: B:H.22 CLA.20: 14 residues within 4Å: Chain B: H.8, H.25, L.28, V.29, W.32, L.460, F.461 Ligands: CLA.11, CLA.14, CLA.18, CLA.19, CLA.21, BCR.24, LHG.29 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:L.28, B:V.29, B:V.29, B:W.32, B:W.32, B:L.460, B:F.461, B:F.461 Salt bridges: B:H.8 pi-Stacking: B:H.25 Metal complexes: B:H.25 CLA.21: 12 residues within 4Å: Chain B: V.7, H.8, V.10, V.21, M.24, H.25, L.28, W.114 Ligands: CLA.18, CLA.19, CLA.20, LMT.27 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:V.7, B:V.21, B:M.24, B:L.28, B:W.114 Metal complexes: B:H.8 CLA.22: 15 residues within 4Å: Chain B: I.19, H.22, L.23, I.137, I.140, H.141, L.144 Chain G: L.12, L.15, N.16 Ligands: CLA.11, CLA.17, CLA.19, CLA.23, BCR.25 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain G, Hydrophobic interactions: B:I.19, B:I.137, B:I.137, B:I.140, B:L.144, G:L.12, G:L.15, G:N.16 Hydrogen bonds: B:H.22 pi-Stacking: B:H.141, B:H.141 Metal complexes: B:H.141 CLA.23: 12 residues within 4Å: Chain B: I.19, L.23, L.106, A.109, W.112, H.113, L.119, L.121 Chain G: T.6, L.8 Ligands: CLA.22, BCR.25 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain G, Hydrophobic interactions: B:I.19, B:L.23, B:L.106, B:A.109, B:W.112, B:L.119, B:L.121, G:L.8 pi-Stacking: B:W.112, B:H.113 Metal complexes: B:H.113 Hydrogen bonds: G:T.6 CLA.30: 23 residues within 4Å: Chain C: L.63, L.136, G.139, A.140, L.143, I.192, M.198, I.201, H.205, I.208, E.212, A.246, M.250, I.253, A.254, M.257, A.264, Y.265 Ligands: CLA.31, CLA.32, CLA.35, CLA.36, BCR.44 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:A.140, C:L.143, C:L.143, C:I.192, C:I.208, C:A.246, C:I.253, C:A.264, C:Y.265 pi-Stacking: C:H.205, C:H.205 Metal complexes: C:H.205 CLA.31: 23 residues within 4Å: Chain C: W.31, L.56, H.59, L.63, Y.65, L.143, F.150, I.247, M.250, G.251, A.254, Y.265, L.394, H.398, L.401, G.402, F.405 Ligands: CLA.30, CLA.32, CLA.33, CLA.38, CLA.39, CLA.41 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:W.31, C:L.56, C:L.63, C:L.143, C:F.150, C:I.247, C:A.254, C:L.394, C:F.405 Hydrogen bonds: C:Y.265 Salt bridges: C:H.59, C:H.398 pi-Stacking: C:H.398 Metal complexes: C:H.398 CLA.32: 17 residues within 4Å: Chain C: V.29, A.32, N.36, L.56, I.60, S.82, H.86, I.247, M.250 Ligands: CLA.30, CLA.31, CLA.36, CLA.38, CLA.39, CLA.41, CLA.42, BOG.47 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:V.29, C:A.32, C:I.247 pi-Stacking: C:H.86, C:H.86 Metal complexes: C:H.86 CLA.33: 11 residues within 4Å: Chain C: W.31, M.35, F.38, Q.52, G.53, I.55, W.393, S.397 Chain I: P.17 Ligands: CLA.31, CLA.39 3 PLIP interactions: 3 interactions with chain C, Hydrophobic interactions: C:W.31, C:I.55, C:W.393 CLA.34: 20 residues within 4Å: Chain A: F.23, I.26, Y.114, M.117, W.121 Chain C: F.232, A.238, S.241, Y.242, V.249, F.406, H.409, L.410, A.413 Chain H: V.12, F.23 Ligands: CLA.5, BOG.7, CLA.36, BCR.44 17 PLIP interactions: 7 interactions with chain C, 9 interactions with chain A, 1 interactions with chain H, Hydrophobic interactions: C:Y.242, C:Y.242, C:V.249, C:F.406, C:L.410, A:F.23, A:F.23, A:I.26, A:Y.114, A:W.121, A:W.121, A:W.121, H:V.12 pi-Stacking: C:H.409, A:W.121, A:W.121 Metal complexes: C:H.409 CLA.35: 16 residues within 4Å: Chain C: L.129, L.133, L.211, E.212, G.215, W.218, H.219, T.222, T.223, P.224, W.225, A.228, F.232 Ligands: CLA.30, CLA.36, BCR.44 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:L.129, C:L.133, C:W.218, C:A.228, C:F.232 Hydrogen bonds: C:W.225 pi-Stacking: C:H.219 Metal complexes: C:H.219 CLA.36: 22 residues within 4Å: Chain C: M.125, T.126, I.128, L.129, H.132, L.133, L.136, I.208, E.212, F.232, W.234, Y.239, Y.242, S.243, A.246, M.250 Ligands: CLA.30, CLA.32, CLA.34, CLA.35, CLA.38, BCR.44 12 PLIP interactions: 11 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:I.128, C:L.129, C:L.136, C:I.208, C:F.232, C:W.234, C:Y.239, C:Y.242, C:Y.242, C:A.246 Hydrogen bonds: C:H.132 Metal complexes: H2O.1 CLA.37: 14 residues within 4Å: Chain C: F.1, W.4, S.5, A.8, L.240, L.244, F.404, F.405, G.408, W.411, H.412, R.415 Ligands: CLA.38, CLA.39 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:A.8, C:L.240, C:L.244, C:L.244, C:F.405 Salt bridges: C:R.415 pi-Stacking: C:W.411, C:H.412, C:H.412 pi-Cation interactions: C:R.415 CLA.38: 23 residues within 4Å: Chain C: N.7, L.10, L.17, A.20, H.21, H.24, W.119, I.128, H.132, L.136, G.236, E.237, Y.239, L.240, S.243, L.244 Ligands: CLA.31, CLA.32, CLA.36, CLA.37, CLA.39, CLA.40, CLA.41 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:L.10, C:L.17, C:A.20, C:H.24, C:W.119, C:I.128, C:H.132, C:L.136, C:Y.239 Hydrogen bonds: C:S.243 pi-Stacking: C:H.21, C:H.21 Metal complexes: C:H.21 CLA.39: 14 residues within 4Å: Chain C: H.24, L.27, I.28, W.31, L.401, F.405 Chain I: P.20, I.24 Ligands: CLA.31, CLA.32, CLA.33, CLA.37, CLA.38, CLA.40 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain I, Hydrophobic interactions: C:L.27, C:I.28, C:W.31, C:L.401, C:F.405, C:F.405, I:P.20 pi-Stacking: C:H.24, C:H.24 Metal complexes: C:H.24 CLA.40: 15 residues within 4Å: Chain C: W.3, W.4, G.6, N.7, R.9, L.10, K.16, A.20, H.24, L.102 Chain I: W.30, Q.31 Ligands: CLA.38, CLA.39, BCR.45 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain I, Hydrophobic interactions: C:W.3, C:L.10, C:L.10, C:K.16, C:L.102 Hydrogen bonds: C:R.9 pi-Stacking: I:W.30, I:W.30 CLA.41: 17 residues within 4Å: Chain C: H.21, A.25, F.114, F.115, Y.117, K.124, I.128, Y.131, H.132, M.135, L.138, G.139 Ligands: CLA.31, CLA.32, CLA.38, CLA.42, BCR.43 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:H.21, C:Y.117, C:I.128, C:I.128, C:I.128, C:Y.131, C:Y.131, C:L.138 pi-Stacking: C:H.132 Metal complexes: C:H.132 CLA.42: 14 residues within 4Å: Chain C: L.18, V.22, V.92, L.93, F.95, G.96, Y.99, H.100, L.108, Y.112, F.115 Ligands: CLA.32, CLA.41, BCR.43 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:L.18, C:L.18, C:V.22, C:V.92, C:L.93, C:F.95, C:Y.99, C:L.108, C:Y.112, C:F.115, C:F.115, C:F.115 pi-Stacking: C:H.100, C:Y.112, C:F.115, C:F.115 pi-Cation interactions: C:H.100 Metal complexes: C:H.100 CLA.48: 20 residues within 4Å: Chain A: T.35, I.39, F.109, V.147, F.148, M.162, I.166, T.169, F.170, M.173 Chain D: M.196, V.199, A.200, L.203, G.204, L.207 Ligands: CLA.2, PHO.4, CLA.51, PL9.54 10 PLIP interactions: 7 interactions with chain A, 2 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: A:T.35, A:I.39, A:F.109, A:V.147, A:F.148, A:T.169, A:F.170, D:V.199, D:L.207 Metal complexes: H2O.1 CLA.51: 25 residues within 4Å: Chain A: M.173, F.196 Chain D: W.46, L.120, P.147, V.150, V.154, F.179, I.180, F.183, Q.184, W.189, T.190, H.195, G.198, V.199, V.202, L.203, L.277, S.280, V.284 Ligands: CLA.2, CLA.3, CLA.48, PHO.49 18 PLIP interactions: 17 interactions with chain D, 1 interactions with chain A, Hydrophobic interactions: D:W.46, D:L.120, D:P.147, D:F.179, D:I.180, D:F.183, D:Q.184, D:W.189, D:V.199, D:V.199, D:V.202, D:L.203, D:L.277, D:L.277, A:F.196 Hydrogen bonds: D:S.280 pi-Stacking: D:W.189 Metal complexes: D:H.195 CLA.52: 15 residues within 4Å: Chain D: L.33, L.34, C.38, F.41, L.88, F.89, V.90, W.91, W.102, A.110, F.111, L.114, H.115, F.118 Ligands: CLA.15 11 PLIP interactions: 11 interactions with chain D, Hydrophobic interactions: D:F.41, D:F.89, D:W.91, D:L.114, D:F.118, D:F.118 Hydrogen bonds: D:V.90 pi-Stacking: D:F.111, D:F.111, D:H.115 Metal complexes: D:H.115

2 x PHO: PHEOPHYTIN A(Non-covalent)

PHO.4: 25 residues within 4Å: Chain A: L.31, A.34, T.35, F.38, F.109, Y.116, E.120, I.133, A.136, Y.137, A.139, P.140, M.162, L.164, G.165, P.269, V.270, I.273 Chain D: L.203, L.207, I.211, W.251, F.255 Ligands: CLA.2, CLA.48 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.31, A:A.34, A:F.38, A:F.109, A:A.139, A:P.140, A:L.164, A:I.273, A:I.273, D:L.203, D:I.211 Hydrogen bonds: A:E.120 PHO.49: 24 residues within 4Å: Chain A: F.196, L.200, M.204, L.248, I.249 Chain D: A.39, L.43, W.46, V.112, G.116, G.119, L.120, F.123, Q.127, N.140, A.143, F.144, A.146, P.147, F.151, G.172, L.277 Ligands: CLA.3, CLA.51 21 PLIP interactions: 20 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:A.39, D:L.43, D:W.46, D:W.46, D:W.46, D:W.46, D:V.112, D:L.120, D:L.120, D:F.123, D:F.123, D:A.143, D:F.144, D:F.144, D:A.146, D:P.147, D:F.151, D:L.277, A:F.196 Hydrogen bonds: D:Q.127, D:N.140

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

BCR.6: 16 residues within 4Å: Chain A: F.7, I.11, V.25, I.28, P.29, L.32, T.33, V.37, I.40, A.44, I.86, L.92, L.96, P.101 Chain H: F.15 Ligands: CLA.5 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain H Hydrophobic interactions: A:F.7, A:I.11, A:I.28, A:L.32, A:T.33, A:V.37, A:I.40, A:I.86, A:L.92, A:L.96, A:P.101, H:F.15, H:F.15 BCR.24: 12 residues within 4Å: Chain B: L.28, G.31, W.32, S.35, I.100, I.101, G.104, L.108 Ligands: CLA.14, CLA.18, CLA.20, LMG.26 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.32, B:I.100, B:L.108 BCR.25: 10 residues within 4Å: Chain B: A.105, L.108, V.111, W.112, T.115, Y.116 Ligands: CLA.13, CLA.22, CLA.23, LMT.28 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.105, B:V.111, B:W.112, B:T.115, B:Y.116 BCR.43: 11 residues within 4Å: Chain C: F.80, V.84, L.85, I.88, S.89, V.92, L.93, F.115 Chain I: Y.6 Ligands: CLA.41, CLA.42 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.80, C:V.84, C:L.85, C:I.88, C:V.92, C:L.93, C:F.115 BCR.44: 15 residues within 4Å: Chain C: I.177, F.178, Y.180, L.181, D.200, I.201, G.204, H.205, I.208, A.231, F.232 Ligands: CLA.30, CLA.34, CLA.35, CLA.36 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.177, C:F.178, C:Y.180, C:L.181, C:I.201, C:I.208, C:A.231, C:F.232 BCR.45: 11 residues within 4Å: Chain C: L.27, F.30, L.37, I.88, S.90, A.91, G.94, V.98 Chain I: Y.6, F.23 Ligands: CLA.40 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain I Hydrophobic interactions: C:L.27, C:F.30, C:L.37, C:I.88, C:A.91, C:V.98, I:Y.6, I:F.23 BCR.53: 13 residues within 4Å: Chain D: Y.40, F.41, G.44, G.45, L.47, T.48, F.99, F.111 Chain F: P.17, T.18, F.21, L.22 Ligands: BOG.55 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain F Hydrophobic interactions: D:Y.40, D:L.47, D:F.99, D:F.111, F:P.17, F:F.21, F:F.21, F:L.22 BCR.57: 12 residues within 4Å: Chain B: L.207 Chain G: M.32, F.35, I.36, L.38, F.39, F.42, I.45 Ligands: CLA.8, CLA.9, CLA.16, CLA.17 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain B Hydrophobic interactions: G:F.35, G:I.36, G:F.39, G:F.39, B:L.207

3 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.7: 11 residues within 4Å: Chain A: F.83, W.87, E.88 Chain C: S.184, F.186, D.189 Chain H: K.5, Y.9 Ligands: CLA.5, CLA.34, DGD.46 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A, 1 interactions with chain H Hydrophobic interactions: C:F.186 Hydrogen bonds: C:S.184, C:S.184, A:W.87, H:K.5 BOG.47: 9 residues within 4Å: Chain C: Y.65, P.78, V.81, S.82, L.85, H.86, S.89, F.150 Ligands: CLA.32 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.85, C:L.85 BOG.55: 8 residues within 4Å: Chain D: Y.65, G.68, C.69, N.70, F.71 Chain F: Q.29, R.33 Ligands: BCR.53 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:Y.65, D:F.71, D:F.71 Hydrogen bonds: F:M.28

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

LMG.26: 6 residues within 4Å: Chain B: T.326, G.327, F.452, G.453 Ligands: CLA.14, BCR.24 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.452 LMG.58: 17 residues within 4Å: Chain B: Y.192, F.249, G.253, W.256, Y.257, Q.276 Chain D: A.84, H.85, I.121, V.152, L.160, G.161 Chain G: L.47, Y.50, N.51 Ligands: CLA.9, CLA.15 10 PLIP interactions: 6 interactions with chain D, 2 interactions with chain G, 2 interactions with chain B Hydrophobic interactions: D:I.121, D:V.152, D:L.160, D:L.160, G:Y.50, G:Y.50 Hydrogen bonds: D:H.85, D:H.85, B:Y.192, B:Q.276

2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.27: 5 residues within 4Å: Chain B: G.1, L.2, W.4, V.7 Ligands: CLA.21 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.4, B:W.4 Hydrogen bonds: B:W.4 LMT.28: 6 residues within 4Å: Chain B: W.90, L.148, F.161 Ligands: CLA.12, CLA.13, BCR.25 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.90, B:L.148

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

LHG.29: 12 residues within 4Å: Chain B: W.4, Y.5, R.6, F.463, W.467 Chain D: Y.139, F.267, V.274, T.275, W.278 Ligands: CLA.18, CLA.20 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:W.4, B:Y.5, D:V.274 Salt bridges: B:R.6

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

DGD.46: 25 residues within 4Å: Chain A: L.81, Y.114, S.145, V.150, I.153 Chain C: P.185, F.186, G.187, G.188, G.190, C.193, S.194, V.195, D.196, C.256, F.260, N.261, N.262, T.263, D.328, F.329, R.330, F.403, F.406 Ligands: BOG.7 14 PLIP interactions: 3 interactions with chain A, 11 interactions with chain C Hydrophobic interactions: A:Y.114, A:V.150, A:I.153, C:F.403, C:F.406 Hydrogen bonds: C:G.188, C:N.262, C:N.262, C:T.263, C:T.263, C:D.328, C:D.328, C:R.330, C:R.330

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

BCT.50: 6 residues within 4Å: Chain A: H.262 Chain D: E.239, T.241, Y.242, K.262 Ligands: FE2.1 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.242

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)

PL9.54: 22 residues within 4Å: Chain A: F.42, I.67 Chain D: M.196, M.197, A.200, L.207, L.208, I.211, H.212, T.215, M.244, N.248, W.251, F.255, V.257, A.258, F.259, L.265, F.268, V.272, T.275 Ligands: CLA.48 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:L.207, D:I.211, D:T.215, D:W.251, D:F.255, D:F.255, D:L.265, D:F.268, D:V.272, A:F.42, A:I.67 Hydrogen bonds: D:F.259

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

HEM.56: 15 residues within 4Å: Chain E: R.2, I.7, R.12, Y.13, I.16, H.17, V.21 Chain F: P.2, I.3, W.8, H.12, A.15, V.16, I.19 Chain K: P.20 16 PLIP interactions: 7 interactions with chain F, 8 interactions with chain E, 1 interactions with chain K, Hydrophobic interactions: F:A.15, F:V.16, F:I.19, E:I.7, E:I.16, E:V.21, K:P.20 Hydrogen bonds: F:I.3 pi-Stacking: F:W.8, F:H.12, E:Y.13, E:H.17 Metal complexes: F:H.12 Salt bridges: E:R.2, E:R.12, E:R.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fadeeva, M. et al., Structure of native photosystem II assembly intermediate from Chlamydomonas reinhardtii . Front Plant Sci (2023)

Release Date

2024-01-31

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
Photosystem II reaction center protein H: G
Photosystem II reaction center protein I: H
Photosystem II reaction center protein K: I
Chain U, Predicted protein: J
Photosystem II reaction center protein Ycf12: K

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
H

H
I

I
K

J
2

K
1

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

Photosystem II reaction center protein H

Photosystem II reaction center protein I

Photosystem II reaction center protein K

Chain U, Predicted protein

Photosystem II reaction center protein Ycf12