SMTL ID : 7dxh.1

Cryo-EM structure of PSII intermediate Psb28-PSII complex

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

7 x MGE: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE(Non-covalent)(Covalent)

MGE.1: 22 residues within 4Å: Chain B: R.10 Chain D: P.3, W.4, Y.5 Chain E: W.256, F.259, F.260, F.263 Chain J: E.11, L.12, N.13, S.16, L.19, G.20, L.23, V.26 Chain K: P.18, F.21 Ligands: CLA.18, MGE.28, PQ9.36, MGE.38 16 PLIP interactions: 5 interactions with chain E, 1 interactions with chain B, 7 interactions with chain J, 1 interactions with chain K, 2 interactions with chain D Hydrophobic interactions: E:W.256, E:F.259, E:F.260, E:F.263, E:F.263, J:L.19, J:L.23, J:L.23, J:L.23, J:V.26, K:F.21, D:W.4, D:W.4 Hydrogen bonds: B:R.10, J:E.11, J:S.16 MGE.27: 18 residues within 4Å: Chain D: Y.39, T.326, G.327, P.328, K.331, A.453, V.456 Chain J: F.35 Chain K: N.4, L.6, A.10, L.13, F.14, V.17 Ligands: CLA.14, BCR.24, BCR.25, LMT.48 11 PLIP interactions: 4 interactions with chain D, 5 interactions with chain K, 2 interactions with chain J Hydrophobic interactions: D:T.326, D:V.456, K:A.10, K:L.13, K:L.13, K:F.14, K:V.17, J:F.35, J:F.35 Hydrogen bonds: D:T.326, D:K.331 MGE.28: 17 residues within 4Å: Chain B: R.10 Chain D: W.4, Y.5, R.6, F.463, W.467, F.478 Chain E: Y.131, R.255, F.259, F.263, V.266, T.267 Ligands: MGE.1, CLA.14, CLA.18, CLA.20 11 PLIP interactions: 6 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:F.259, E:F.263, E:V.266, D:W.4, D:F.463, D:F.463 Hydrogen bonds: E:Y.131, E:Y.131, E:R.255, D:Y.5 Salt bridges: D:R.6 MGE.38: 19 residues within 4Å: Chain E: F.247, I.249, A.250, F.251, S.252, N.253, W.256 Chain J: T.15, Y.18, L.19, L.22, V.26 Chain L: F.10, I.13, F.17, A.20, I.21 Ligands: MGE.1, PQ9.36 13 PLIP interactions: 5 interactions with chain E, 4 interactions with chain J, 4 interactions with chain L Hydrophobic interactions: E:F.247, E:I.249, E:F.251, E:F.251, J:Y.18, J:L.22, J:V.26, L:F.10, L:I.13, L:F.17, L:F.17 Hydrogen bonds: E:S.252, J:T.15 MGE.42: 12 residues within 4Å: Chain E: L.39, Y.57, G.60, C.61, F.63 Chain G: L.26, T.30, I.37, M.40, Q.41 Ligands: DGD.7, BCR.37 7 PLIP interactions: 4 interactions with chain G, 3 interactions with chain E Hydrophobic interactions: G:L.26, G:T.30, E:L.39, E:F.63 Hydrogen bonds: G:M.40, G:Q.41, E:F.63 MGE.49: 4 residues within 4Å: Chain K: L.16, E.30 Chain L: F.19 Ligands: SQD.47 5 PLIP interactions: 2 interactions with chain K, 3 interactions with chain L Hydrophobic interactions: K:L.16, L:F.19, L:F.19, L:F.19 Hydrogen bonds: K:E.30 MGE.52: 19 residues within 4Å: Chain C: F.93, W.97, E.98, F.117, L.120, S.124, F.155 Chain I: K.5, Y.9 Chain N: L.191, L.192, K.193, S.194, P.195, F.196, E.199, W.201 Ligands: CLA.4, DGD.66 8 PLIP interactions: 4 interactions with chain N, 2 interactions with chain I, 2 interactions with chain C Hydrophobic interactions: N:P.195, N:W.201, N:W.201, C:F.117, C:L.120 Hydrogen bonds: N:E.199, I:Y.9, I:Y.9

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

SQD.2: 4 residues within 4Å: Chain C: W.20, N.26, L.28, V.30 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.20, C:V.30 Hydrogen bonds: C:L.28 SQD.47: 11 residues within 4Å: Chain J: R.14, L.17, Y.18 Chain K: I.23, Y.26, V.27, E.30 Chain L: A.15, L.16, F.19 Ligands: MGE.49 9 PLIP interactions: 2 interactions with chain K, 3 interactions with chain L, 4 interactions with chain J Hydrophobic interactions: K:I.23, K:V.27, L:L.16, L:F.19, L:F.19, J:L.17, J:Y.18 Salt bridges: J:R.14, J:R.14

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

CLA.3: 25 residues within 4Å: Chain C: Y.147, P.150, S.153, V.157, F.182, M.183, F.186, Q.187, I.192, H.198, G.201, V.202, V.205, F.206, V.283, A.286, A.287, I.290 Chain E: L.172, L.195 Chain L: F.17 Ligands: CLA.8, PHO.29, CLA.30, CLA.34 10 PLIP interactions: 3 interactions with chain E, 6 interactions with chain C, 1 interactions with chain L, Hydrophobic interactions: E:L.172, E:L.172, E:L.195, C:F.186, C:Q.187, C:I.192, C:V.202, C:V.205, C:F.206, L:F.17 CLA.4: 20 residues within 4Å: Chain C: I.36, P.39, T.40, F.93, Y.94, P.95, I.96, Q.113, L.114, F.117, H.118, L.121 Chain I: V.8, Y.9, V.11, V.12, T.13, F.15 Ligands: BCR.5, MGE.52 14 PLIP interactions: 4 interactions with chain I, 10 interactions with chain C, Hydrophobic interactions: I:Y.9, I:V.11, I:T.13, I:F.15, C:I.36, C:P.39, C:T.40, C:F.93, C:P.95, C:I.96, C:L.114, C:F.117 Hydrogen bonds: C:I.96 Salt bridges: C:H.118 CLA.8: 17 residues within 4Å: Chain C: Q.199, V.202, A.203, F.206, G.207, L.210, W.278 Chain E: F.147, F.163, V.165, I.168, F.169, F.171, L.172 Ligands: CLA.3, PHO.31, CLA.34 10 PLIP interactions: 6 interactions with chain E, 4 interactions with chain C, Hydrophobic interactions: E:F.147, E:F.163, E:I.168, E:F.171, E:L.172, E:L.172, C:V.202, C:L.210, C:W.278 pi-Stacking: C:F.206 CLA.9: 24 residues within 4Å: Chain D: G.188, F.189, P.191, G.196, H.200, A.203, V.207, F.245, F.246, F.249, V.250, T.254 Chain E: L.148 Chain H: F.37, F.40, I.44, L.45, Y.48 Ligands: CLA.10, CLA.12, CLA.16, CLA.43, BCR.45, DGD.46 16 PLIP interactions: 4 interactions with chain H, 11 interactions with chain D, 1 interactions with chain E, Hydrophobic interactions: H:F.37, H:F.40, H:I.44, D:F.189, D:F.189, D:P.191, D:H.200, D:A.203, D:V.207, D:F.245, D:F.246, D:F.246, D:F.249, D:V.250, E:L.148 pi-Stacking: H:F.40 CLA.10: 23 residues within 4Å: Chain D: R.67, L.68, A.145, F.152, H.200, H.201, A.243, F.246, A.247, V.250, V.251, T.261 Chain H: M.34, F.37, L.38 Ligands: CLA.9, CLA.11, CLA.12, CLA.13, CLA.15, CLA.16, CLA.17, BCR.45 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain H, Hydrophobic interactions: D:F.152, D:F.152, D:F.152, D:A.243, D:F.246, D:F.246, D:A.247, D:V.250, D:V.251, H:F.37, H:L.38 Hydrogen bonds: D:R.67 Salt bridges: D:R.67 pi-Stacking: D:H.200 CLA.11: 25 residues within 4Å: Chain D: W.32, F.60, F.64, R.67, L.144, L.147, L.148, V.244, A.247, A.248, V.251, F.450, H.454, F.457, A.458, F.461 Ligands: CLA.10, CLA.12, CLA.13, CLA.14, CLA.18, CLA.19, CLA.20, CLA.22, BCR.25 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:W.32, D:F.60, D:F.64, D:L.144, D:L.147, D:L.148, D:V.244, D:A.247, D:V.251, D:F.450, D:F.450, D:F.457, D:F.457, D:F.457, D:F.461, D:F.461 Salt bridges: D:R.67 CLA.12: 23 residues within 4Å: Chain D: T.26, V.29, A.30, W.32, A.33, A.37, V.61, F.64, M.65, R.67, L.68, H.99, L.142, A.204 Ligands: CLA.9, CLA.10, CLA.11, CLA.13, CLA.16, CLA.17, CLA.19, CLA.22, BCR.26 6 PLIP interactions: 6 interactions with chain D, Hydrophobic interactions: D:V.29, D:W.32, D:A.33, D:L.68, D:L.142 Salt bridges: D:R.67 CLA.13: 23 residues within 4Å: Chain D: L.68, G.69, V.70, F.89, W.90, V.95, A.98, H.99, V.101, L.102, L.105, L.148, G.151, F.152, F.155, H.156, F.161, G.162, P.163 Ligands: CLA.10, CLA.11, CLA.12, BCR.26 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:L.68, D:L.68, D:F.89, D:F.89, D:W.90, D:W.90, D:W.90, D:A.98, D:V.101, D:L.102, D:L.102, D:L.105, D:L.148, D:F.152, D:F.155, D:F.161 Salt bridges: D:H.99 pi-Stacking: D:W.90 CLA.14: 28 residues within 4Å: Chain D: W.32, M.36, Y.39, Q.57, G.58, M.59, F.60, L.323, F.324, T.326, G.327, P.328, P.446, W.449, F.450, A.453, H.454 Chain E: T.267, M.271 Chain J: F.31, F.35 Chain K: F.14 Ligands: CLA.11, CLA.20, BCR.24, BCR.25, MGE.27, MGE.28 13 PLIP interactions: 9 interactions with chain D, 1 interactions with chain K, 2 interactions with chain J, 1 interactions with chain E, Hydrophobic interactions: D:Y.39, D:F.60, D:F.324, D:P.446, D:W.449, D:W.449, D:W.449, K:F.14, J:F.31, J:F.35, E:T.267 Hydrogen bonds: D:G.327 pi-Stacking: D:F.60 CLA.15: 24 residues within 4Å: Chain D: T.235, S.238, S.239, A.242, F.245, F.246, F.462, H.465, G.469, T.472, L.473 Chain E: L.26, L.79, F.110, I.113, M.116, L.117, F.120 Ligands: CLA.10, CLA.16, CLA.17, CLA.35, UNL.40, DGD.46 19 PLIP interactions: 9 interactions with chain E, 10 interactions with chain D, Hydrophobic interactions: E:L.79, E:L.79, E:F.110, E:F.110, E:F.110, E:I.113, E:M.116, E:L.117, E:F.120, D:A.242, D:F.245, D:F.245, D:F.246, D:F.462, D:F.462, D:L.473 Hydrogen bonds: D:S.238 Salt bridges: D:H.465 pi-Stacking: D:H.465 CLA.16: 22 residues within 4Å: Chain D: F.138, V.207, A.211, F.214, H.215, V.218, R.219, P.220, P.221, L.224, L.228 Chain E: F.110 Chain H: T.26, M.30, F.33 Ligands: CLA.9, CLA.10, CLA.12, CLA.15, CLA.17, UNL.40, BCR.45 11 PLIP interactions: 7 interactions with chain D, 3 interactions with chain H, 1 interactions with chain E, Hydrophobic interactions: D:F.138, D:F.138, D:F.138, D:V.207, D:A.211, D:F.214, D:L.228, H:M.30, H:F.33, E:F.110 Hydrogen bonds: H:T.26 CLA.17: 20 residues within 4Å: Chain D: H.22, L.134, M.137, F.138, H.141, L.142, A.145, M.230, I.233, V.236, S.239, S.240, A.243, V.244 Ligands: CLA.10, CLA.12, CLA.15, CLA.16, CLA.19, CLA.22 8 PLIP interactions: 8 interactions with chain D, Hydrophobic interactions: D:L.134, D:M.137, D:F.138, D:A.145, D:M.230, D:I.233, D:V.236, D:V.244 CLA.18: 25 residues within 4Å: Chain B: N.12 Chain D: W.4, Y.5, R.6, V.7, H.8, T.9, L.237, I.241, F.457, L.460, F.461, F.463, G.464, W.467, H.468, R.471 Chain K: F.21 Ligands: MGE.1, CLA.11, CLA.19, CLA.20, CLA.21, BCR.25, MGE.28 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain K, Hydrophobic interactions: D:T.9, D:I.241, D:F.457, D:F.461, D:F.461, D:F.463, K:F.21 Hydrogen bonds: D:V.7, D:H.8 Salt bridges: D:H.8, D:R.471 pi-Stacking: D:W.467 CLA.19: 20 residues within 4Å: Chain D: H.8, L.11, I.12, L.18, H.22, H.25, T.26, I.233, V.236, L.237, S.240, I.241, V.244 Ligands: CLA.11, CLA.12, CLA.17, CLA.18, CLA.20, CLA.21, CLA.22 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:H.8, D:L.11, D:H.22, D:T.26, D:I.233, D:V.236, D:L.237, D:L.237, D:V.244 Hydrogen bonds: D:S.240 Salt bridges: D:H.22 Metal complexes: D:H.22 CLA.20: 13 residues within 4Å: Chain D: H.8, H.25, W.32, V.244, F.461 Ligands: CLA.11, CLA.14, CLA.18, CLA.19, CLA.21, BCR.24, BCR.25, MGE.28 6 PLIP interactions: 6 interactions with chain D, Hydrophobic interactions: D:W.32, D:V.244, D:F.461 Salt bridges: D:H.8, D:H.8 Metal complexes: D:H.25 CLA.21: 16 residues within 4Å: Chain D: L.2, V.7, H.8, V.10, L.11, A.21, L.28, W.114 Chain J: Q.8, V.10 Chain K: F.21, L.25 Ligands: CLA.18, CLA.19, CLA.20, BCR.24 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain K, Hydrophobic interactions: D:V.7, D:L.11, D:L.28, D:W.114, K:F.21, K:L.25 CLA.22: 17 residues within 4Å: Chain D: I.19, H.22, L.23, L.121, L.132, M.137, I.140, H.141, L.144 Chain H: L.6, L.13 Ligands: CLA.11, CLA.12, CLA.17, CLA.19, CLA.23, BCR.26 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain H, Hydrophobic interactions: D:I.19, D:L.121, D:L.132, D:I.140, D:L.144, H:L.6, H:L.13 Hydrogen bonds: D:H.22 Metal complexes: D:H.141 CLA.23: 13 residues within 4Å: Chain D: I.19, L.23, L.106, A.109, W.112, H.113, L.119, L.121 Chain H: T.4, L.6, G.7 Ligands: CLA.22, BCR.26 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain H, Hydrophobic interactions: D:I.19, D:I.19, D:L.23, D:L.106, D:W.112, D:W.112, D:L.119, D:L.121, H:L.6 pi-Stacking: D:W.112 Metal complexes: D:H.113 Hydrogen bonds: H:T.4 CLA.30: 20 residues within 4Å: Chain C: T.45, F.48, M.172, I.176, F.180, F.182, M.183 Chain E: H.187, M.188, V.191, A.192, L.195, G.196, L.199 Chain J: L.30 Chain L: F.10 Ligands: CLA.3, PHO.29, CLA.34, PQ9.36 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain E, 1 interactions with chain L, Hydrophobic interactions: C:F.48, C:F.180, C:F.182, E:V.191, L:F.10 CLA.34: 27 residues within 4Å: Chain C: M.183, F.206 Chain E: L.35, L.112, P.139, V.142, F.143, S.145, V.146, F.171, L.172, F.175, Q.176, W.181, T.182, H.187, G.190, V.191, V.194, L.269, S.272, A.273, V.276 Ligands: CLA.3, CLA.8, CLA.30, PHO.31 18 PLIP interactions: 17 interactions with chain E, 1 interactions with chain C, Hydrophobic interactions: E:L.35, E:L.112, E:P.139, E:V.142, E:F.171, E:L.172, E:L.172, E:F.175, E:Q.176, E:T.182, E:V.191, E:V.191, E:V.194, E:V.194, E:L.269, E:L.269, C:F.206 pi-Stacking: E:W.181 CLA.35: 21 residues within 4Å: Chain E: P.29, C.30, L.33, L.79, L.80, L.81, L.82, W.83, W.94, T.102, F.103, L.106, H.107 Chain H: L.38, L.42 Chain M: G.12, L.13, G.16, A.17, V.19 Ligands: CLA.15 13 PLIP interactions: 2 interactions with chain H, 8 interactions with chain E, 3 interactions with chain M, Hydrophobic interactions: H:L.38, H:L.42, E:P.29, E:L.82, E:W.83, E:W.83, E:W.83, E:L.106, M:L.13, M:V.19, M:V.19 Hydrogen bonds: E:L.82 Salt bridges: E:H.107 CLA.43: 8 residues within 4Å: Chain D: G.185, P.186, F.189, A.203 Chain H: F.40, I.43 Ligands: CLA.9, BCR.45 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain D, Hydrophobic interactions: H:F.40, D:P.186, D:A.203 CLA.53: 23 residues within 4Å: Chain N: T.72, L.73, L.146, G.149, A.150, L.153, L.163, W.201, V.211, H.215, I.218, A.256, M.260, I.263, F.267, V.274, Y.275 Ligands: CLA.54, CLA.55, CLA.57, CLA.58, CLA.59, BCR.65 12 PLIP interactions: 12 interactions with chain N, Hydrophobic interactions: N:A.150, N:L.153, N:L.153, N:W.201, N:I.218, N:A.256, N:M.260, N:I.263, N:F.267, N:V.274, N:V.274 Hydrogen bonds: N:Y.275 CLA.54: 20 residues within 4Å: Chain N: W.41, H.69, L.73, L.152, L.153, F.160, L.257, M.260, A.264, V.268, Y.275, L.404, H.408, L.411, F.415 Ligands: CLA.53, CLA.55, CLA.56, CLA.61, CLA.62 12 PLIP interactions: 12 interactions with chain N, Hydrophobic interactions: N:W.41, N:L.73, N:L.153, N:F.160, N:L.257, N:M.260, N:A.264, N:L.404, N:F.415 Salt bridges: N:H.69, N:H.408 pi-Stacking: N:H.408 CLA.55: 18 residues within 4Å: Chain N: I.38, V.39, W.41, A.42, T.46, L.66, H.69, I.70, W.75, V.92, H.96, L.257, M.260 Ligands: CLA.53, CLA.54, CLA.60, CLA.61, CLA.62 8 PLIP interactions: 8 interactions with chain N, Hydrophobic interactions: N:V.39, N:A.42, N:W.75, N:V.92, N:L.257 Salt bridges: N:H.69, N:H.96 Metal complexes: N:H.96 CLA.56: 14 residues within 4Å: Chain N: W.41, M.45, F.48, Q.62, G.63, I.65, L.382, W.403, L.404, S.407 Chain O: P.26, V.30 Ligands: CLA.54, DGD.67 7 PLIP interactions: 1 interactions with chain O, 6 interactions with chain N, Hydrophobic interactions: O:V.30, N:W.41, N:F.48, N:W.403, N:W.403, N:L.404 pi-Stacking: N:W.41 CLA.57: 16 residues within 4Å: Chain C: F.33, W.131 Chain I: F.23 Chain N: A.248, Y.252, G.255, A.256, M.259, L.416, H.419, L.420, A.423, R.427 Ligands: CLA.53, CLA.59, BCR.65 9 PLIP interactions: 8 interactions with chain N, 1 interactions with chain C, Hydrophobic interactions: N:Y.252, N:A.256, N:L.416, N:L.416, N:L.420, N:A.423, C:W.131 Salt bridges: N:R.427 pi-Stacking: N:H.419 CLA.58: 14 residues within 4Å: Chain N: L.139, L.143, I.221, C.222, G.225, W.228, H.229, T.232, T.233, F.235, F.242 Ligands: CLA.53, CLA.59, BCR.65 7 PLIP interactions: 7 interactions with chain N, Hydrophobic interactions: N:L.139, N:L.139, N:L.143, N:L.143, N:I.221 Hydrogen bonds: N:F.235 Metal complexes: N:H.229 CLA.59: 16 residues within 4Å: Chain N: M.135, L.139, H.142, L.143, L.146, F.242, W.244, Y.249, Y.252, S.253, M.260 Ligands: CLA.53, CLA.57, CLA.58, CLA.60, BCR.65 9 PLIP interactions: 9 interactions with chain N, Hydrophobic interactions: N:L.139, N:L.146, N:F.242, N:F.242, N:W.244, N:W.244, N:Y.249, N:Y.252 Salt bridges: N:H.142 CLA.60: 15 residues within 4Å: Chain N: N.17, L.20, L.27, H.31, H.34, I.38, E.247, Y.249, L.250, S.253, L.254, L.257 Ligands: CLA.55, CLA.59, CLA.61 9 PLIP interactions: 9 interactions with chain N, Hydrophobic interactions: N:N.17, N:L.20, N:L.27, N:E.247, N:Y.249, N:L.250, N:L.250 Hydrogen bonds: N:S.253 Metal complexes: N:H.31 CLA.61: 15 residues within 4Å: Chain N: H.34, I.38, L.250, L.257, L.411, F.414, F.415, W.421, H.422 Chain O: V.30, L.33 Ligands: CLA.54, CLA.55, CLA.60, CLA.68 12 PLIP interactions: 9 interactions with chain N, 3 interactions with chain O, Hydrophobic interactions: N:I.38, N:L.250, N:L.257, N:F.414, N:F.415, N:F.415, N:W.421, O:V.30, O:V.30, O:L.33 Salt bridges: N:H.422 Metal complexes: N:H.34 CLA.62: 14 residues within 4Å: Chain N: H.31, A.35, L.103, F.125, Y.127, I.138, F.141, H.142, V.145, G.149 Ligands: CLA.54, CLA.55, CLA.63, BCR.69 8 PLIP interactions: 8 interactions with chain N, Hydrophobic interactions: N:H.31, N:F.125, N:F.125, N:Y.127, N:I.138, N:I.138, N:F.141, N:V.145 CLA.63: 13 residues within 4Å: Chain N: L.28, V.32, V.102, F.105, G.106, Y.109, H.110, P.115, Y.121, F.125 Chain P: W.47 Ligands: CLA.62, BCR.69 10 PLIP interactions: 9 interactions with chain N, 1 interactions with chain P, Hydrophobic interactions: N:V.32, N:V.32, N:F.105, N:Y.109, N:F.125, N:F.125, P:W.47 Hydrogen bonds: N:Y.109 Salt bridges: N:H.110 pi-Stacking: N:H.110 CLA.68: 17 residues within 4Å: Chain N: Q.6, G.16, N.17, R.19, L.20, L.23, K.26, A.33, L.37, A.111 Chain O: L.33, A.36, W.39, Q.40 Chain P: A.26 Ligands: CLA.61, BCR.64 11 PLIP interactions: 7 interactions with chain N, 4 interactions with chain O, Hydrophobic interactions: N:L.20, N:K.26, N:A.33, N:L.37, N:A.111, O:L.33, O:A.36, O:W.39 Hydrogen bonds: N:Q.6, N:R.19 pi-Stacking: O:W.39

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

BCR.5: 17 residues within 4Å: Chain C: V.35, I.38, P.39, L.42, A.43, I.46, C.47, I.50, A.51, A.54, I.96, L.102, W.105, L.106, P.111 Chain I: F.15 Ligands: CLA.4 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:V.35, C:I.38, C:P.39, C:A.43, C:I.46, C:I.50, C:A.51, C:I.96, C:L.102, C:W.105, C:L.106, C:L.106, C:P.111 BCR.24: 13 residues within 4Å: Chain D: M.24, L.28, F.107, C.111, W.114 Chain K: L.6, L.13 Ligands: CLA.14, CLA.20, CLA.21, BCR.25, MGE.27, LMT.48 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain K Hydrophobic interactions: D:M.24, D:L.28, D:L.28, D:F.107, D:W.114, D:W.114, K:L.6, K:L.13 BCR.25: 14 residues within 4Å: Chain D: L.28, G.31, W.32, S.35, I.100, V.101, S.103, G.104 Ligands: CLA.11, CLA.14, CLA.18, CLA.20, BCR.24, MGE.27 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.101 BCR.26: 12 residues within 4Å: Chain D: W.90, L.105, L.108, A.109, C.111, W.112, V.115, Y.116 Ligands: CLA.12, CLA.13, CLA.22, CLA.23 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:W.90, D:W.90, D:L.108, D:A.109, D:W.112, D:V.115, D:Y.116 BCR.37: 15 residues within 4Å: Chain E: Y.32, L.33, G.36, G.37, L.39, T.40, F.91, W.94, L.100, F.103 Chain G: P.29, T.30, F.33, L.34 Ligands: MGE.42 12 PLIP interactions: 8 interactions with chain E, 4 interactions with chain G Hydrophobic interactions: E:Y.32, E:L.39, E:T.40, E:F.91, E:W.94, E:L.100, E:F.103, E:F.103, G:P.29, G:F.33, G:F.33, G:L.34 BCR.45: 14 residues within 4Å: Chain H: F.33, M.34, L.36, F.37, V.39, F.40, I.43 Chain M: I.2, L.6, F.10 Ligands: CLA.9, CLA.10, CLA.16, CLA.43 9 PLIP interactions: 3 interactions with chain M, 6 interactions with chain H Hydrophobic interactions: M:I.2, M:L.6, M:F.10, H:F.33, H:F.37, H:F.37, H:V.39, H:F.40, H:F.40 BCR.64: 16 residues within 4Å: Chain N: G.36, L.37, F.40, F.90, L.97, I.98, S.100, A.101 Chain O: Y.15, L.21, F.32, W.39 Chain P: F.5, L.12 Ligands: CLA.68, BCR.69 15 PLIP interactions: 7 interactions with chain N, 6 interactions with chain O, 2 interactions with chain P Hydrophobic interactions: N:L.37, N:F.40, N:F.90, N:L.97, N:L.97, N:I.98, N:A.101, O:Y.15, O:Y.15, O:L.21, O:F.32, O:F.32, O:W.39, P:F.5, P:L.12 BCR.65: 12 residues within 4Å: Chain N: I.187, Y.190, I.202, V.205, G.214, H.215, I.218, F.242 Ligands: CLA.53, CLA.57, CLA.58, CLA.59 7 PLIP interactions: 7 interactions with chain N Hydrophobic interactions: N:I.187, N:Y.190, N:I.202, N:V.205, N:I.218, N:I.218, N:F.242 BCR.69: 13 residues within 4Å: Chain N: V.91, V.94, V.95, I.98, S.99, V.102 Chain P: V.54, L.57, N.58, V.61 Ligands: CLA.62, CLA.63, BCR.64 6 PLIP interactions: 4 interactions with chain N, 2 interactions with chain P Hydrophobic interactions: N:V.91, N:V.94, N:I.98, N:V.102, P:L.57, P:V.61

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain C: N.181, H.332 Chain E: K.307 Ligand excluded by PLIP CL.51: 2 residues within 4Å: Chain N: Q.291, E.332 Ligand excluded by PLIP

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

DGD.7: 11 residues within 4Å: Chain C: P.196, F.197, Q.199, L.200, A.203, F.302 Chain E: N.62 Chain N: L.382, N.383 Ligands: MGE.42, DGD.67 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:P.196, C:F.197, C:Q.199, C:L.200, C:A.203, C:F.302 Hydrogen bonds: E:N.62 DGD.46: 24 residues within 4Å: Chain D: Y.192, F.249, G.253, Y.257, Y.272, Q.273, S.276, Y.278, F.462 Chain E: G.76, H.77, A.109, I.113, V.144, L.152, S.155 Chain H: L.45, Y.48, N.49, V.59, S.60, W.61 Ligands: CLA.9, CLA.15 13 PLIP interactions: 6 interactions with chain E, 3 interactions with chain D, 4 interactions with chain H Hydrophobic interactions: E:A.109, E:V.144, E:L.152, D:Y.257, D:F.462, H:L.45, H:Y.48 Hydrogen bonds: E:H.77, E:H.77, E:S.155, D:S.276, H:V.59, H:W.61 DGD.66: 27 residues within 4Å: Chain C: L.91, A.152, L.159, I.160, I.163 Chain N: P.195, F.196, G.197, G.198, E.199, G.200, W.201, V.203, S.204, V.205, N.206, F.262, I.263, C.266, F.270, N.271, N.272, T.273, D.338, R.340, F.413 Ligands: MGE.52 16 PLIP interactions: 12 interactions with chain N, 4 interactions with chain C Hydrophobic interactions: N:P.195, N:F.196, N:F.196, N:F.262, N:I.263, N:F.413, C:A.152, C:L.159, C:I.163, C:I.163 Hydrogen bonds: N:G.198, N:G.200, N:W.201, N:I.202, N:N.272, N:T.273 DGD.67: 10 residues within 4Å: Chain C: F.197, T.292 Chain N: L.382, S.384, W.403, T.406, S.407, V.410 Ligands: DGD.7, CLA.56 5 PLIP interactions: 3 interactions with chain N, 2 interactions with chain C Hydrophobic interactions: N:L.382, N:V.410, C:F.197, C:T.292 Hydrogen bonds: N:S.384

2 x PHO: PHEOPHYTIN A(Non-covalent)

PHO.29: 25 residues within 4Å: Chain C: L.41, A.44, T.45, F.48, I.115, F.119, Y.126, Q.130, A.146, Y.147, P.150, L.174, G.175, R.279, V.283 Chain E: L.195, A.198, L.199, A.202, I.203, W.243, F.247 Ligands: CLA.3, CLA.30, PQ9.36 19 PLIP interactions: 7 interactions with chain E, 12 interactions with chain C Hydrophobic interactions: E:L.195, E:L.195, E:L.199, E:L.199, E:A.202, E:I.203, E:I.203, C:L.41, C:A.44, C:F.48, C:I.115, C:F.119, C:F.119, C:A.146, C:Y.147, C:Y.147, C:R.279, C:V.283 Hydrogen bonds: C:Q.130 PHO.31: 26 residues within 4Å: Chain C: F.206, A.209, L.210, M.214 Chain E: L.35, W.38, I.104, G.108, G.111, L.112, F.115, Q.119, N.132, A.135, F.136, P.139, F.143, F.163, G.164, V.165, I.168, P.265, V.266, L.269 Ligands: CLA.8, CLA.34 19 PLIP interactions: 18 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:L.35, E:W.38, E:I.104, E:L.112, E:F.115, E:A.135, E:F.136, E:F.136, E:P.139, E:F.143, E:F.163, E:F.163, E:V.165, E:I.168, E:P.265, E:V.266, E:L.269, C:F.206 Hydrogen bonds: E:N.132

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

LMT.32: 6 residues within 4Å: Chain C: A.54, L.72, Y.73, G.74 Chain E: R.294 Ligands: LMT.50 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.54 Hydrogen bonds: C:Y.73 LMT.48: 4 residues within 4Å: Chain D: Y.39 Chain K: L.6 Ligands: BCR.24, MGE.27 No protein-ligand interaction detected (PLIP) LMT.50: 7 residues within 4Å: Chain C: V.49, I.50, I.53, L.72 Chain L: M.1, I.4 Ligands: LMT.32 6 PLIP interactions: 3 interactions with chain L, 3 interactions with chain C Hydrophobic interactions: L:I.4, C:V.49, C:I.50, C:I.53 Hydrogen bonds: L:M.1, L:M.1

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

FE2.33: 5 residues within 4Å: Chain C: H.215, H.272 Chain E: H.204, E.231, H.258 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain C Metal complexes: E:H.204, E:E.231, E:H.258, C:H.215

1 x PQ9: 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE(Non-covalent)

PQ9.36: 23 residues within 4Å: Chain C: I.176 Chain E: M.189, A.192, L.200, H.204, T.207, Y.234, M.236, A.239, N.240, W.243, F.247, I.249, A.250, F.251, L.257, F.260, V.264 Chain J: L.29 Ligands: MGE.1, PHO.29, CLA.30, MGE.38 13 PLIP interactions: 11 interactions with chain E, 1 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: E:M.189, E:L.200, E:Y.234, E:F.247, E:F.251, E:L.257, E:F.260, E:V.264, E:V.264, C:I.176, J:L.29 Hydrogen bonds: E:T.207, E:F.251

2 x UNL: UNKNOWN LIGAND

UNL.39: 10 residues within 4Å: Chain E: W.22, S.23, L.26, L.117, F.120, E.121, R.124 Chain H: L.38 Chain M: L.20 Ligands: UNL.40 6 PLIP interactions: 4 interactions with chain E, 1 interactions with chain H, 1 interactions with chain M Hydrophobic interactions: E:L.26, E:L.117, E:L.117, E:F.120, H:L.38, M:L.20 UNL.40: 11 residues within 4Å: Chain D: A.227, L.228, R.229 Chain E: F.5, D.9, K.13, W.22 Chain H: M.34 Ligands: CLA.15, CLA.16, UNL.39 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:F.5, E:W.22, E:W.22, E:W.22, D:L.228 Salt bridges: E:K.13, D:R.229

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

HEM.41: 7 residues within 4Å: Chain F: H.23, I.25, T.26, I.27 Chain G: V.23, H.24, V.28 7 PLIP interactions: 4 interactions with chain F, 3 interactions with chain G, Hydrophobic interactions: F:H.23, F:T.26, F:I.27, G:V.28 Salt bridges: F:H.23 pi-Stacking: G:W.20 pi-Cation interactions: G:H.24

1 x HTG: heptyl 1-thio-beta-D-glucopyranoside(Non-covalent)

HTG.44: 4 residues within 4Å: Chain E: W.4, F.5 Chain H: W.24, P.28 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.5 Hydrogen bonds: E:W.4, E:F.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, Y. et al., Structural insights into cyanobacterial photosystem II intermediates associated with Psb28 and Tsl0063. Nat.Plants (2021)

Release Date

2021-06-30

Peptides

Photosystem II reaction center Psb28 protein: A
Tsl0063 protein: B
Photosystem II protein D1: C
Photosystem II CP47 reaction center protein: D
Photosystem II D2 protein: E
Cytochrome b559 subunit alpha: F
Cytochrome b559 subunit beta: G
Photosystem II reaction center protein H: H
Photosystem II reaction center protein I: I
Photosystem II reaction center protein L: J
Photosystem II reaction center protein M: K
Photosystem II reaction center protein T: L
Photosystem II reaction center protein X: M
Photosystem II CP43 reaction center protein: N
Photosystem II reaction center protein K: O
Photosystem II reaction center protein Z: P
Photosystem II reaction center protein Ycf12: Q
unidentified transmembrane protein: R

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
a

D
b

E
d

F
e

G
f

H
h

I
i

J
l

K
m

L
t

M
x

N
c

O
k

P
z

Q
y

R
C

Membrane

We predict this structure to be a membrane protein.
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Photosystem II reaction center Psb28 protein

Tsl0063 protein

Photosystem II protein D1

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 L

Photosystem II reaction center protein M

Photosystem II reaction center protein T

Photosystem II reaction center protein X

Photosystem II CP43 reaction center protein

Photosystem II reaction center protein K

Photosystem II reaction center protein Z

Photosystem II reaction center protein Ycf12

unidentified transmembrane protein

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