SMTL ID : 8w4o.1

Structure of PSII-FCPII-G/H complex in the PSII-FCPII supercomplex from Cyclotella meneghiniana

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

6 x A86: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate(Non-covalent)

A86.1: 7 residues within 4Å: Chain A: P.11, V.12, Q.134, L.141 Ligands: CLA.4, CLA.5, CLA.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.12, A:L.141 Hydrogen bonds: A:Q.134 A86.3: 17 residues within 4Å: Chain A: Q.44, V.47, I.51, L.115, G.116, Q.135, L.138, A.139, A.142, E.146, Q.149, L.161 Ligands: CLA.10, CLA.11, CLA.12, CLA.14, LHG.18 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Q.44, A:V.47, A:I.51, A:L.138, A:L.138, A:A.142, A:E.146 Hydrogen bonds: A:Q.149 A86.20: 12 residues within 4Å: Chain A: I.52, K.55 Chain C: A.9, P.10, T.11, Q.124, L.131 Ligands: SQD.19, CLA.41, CLA.42, CLA.49, CLA.51 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.131 Hydrogen bonds: C:T.11, C:Q.124 A86.21: 8 residues within 4Å: Chain B: P.10, Q.124, L.128, L.131 Ligands: CLA.25, CLA.26, CLA.32, CLA.34 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.131 Hydrogen bonds: B:P.10, B:Q.124 A86.22: 13 residues within 4Å: Chain B: K.37, L.44, F.59, D.60, I.61, I.88, I.92, D.96 Ligands: CLA.27, CLA.28, CLA.29, CLA.30, CLA.33 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:K.37, B:L.44, B:F.59, B:I.88, B:I.92, B:I.92 Hydrogen bonds: B:D.96 A86.38: 13 residues within 4Å: Chain C: K.37, V.41, L.44, F.59, D.60, I.88, I.92, D.96 Ligands: CLA.44, CLA.45, CLA.46, CLA.47, CLA.50 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:K.37, C:V.41, C:F.59, C:F.59, C:I.88, C:I.92, C:D.96

1 x ET4: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol(Non-covalent)

ET4.2: 18 residues within 4Å: Chain A: F.15, D.16, P.17, A.18, G.19, F.20, H.39, A.43, A.46, F.50, A.73, V.76, M.140, F.143 Ligands: CLA.5, CLA.6, CLA.7, CLA.9 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.15, A:A.18, A:F.20, A:A.46, A:F.50, A:M.140, A:F.143 Hydrogen bonds: A:A.18, A:G.19, A:A.73

36 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.4: 9 residues within 4Å: Chain A: L.9, P.10, P.11, V.130, R.131, Q.134, Q.135 Ligands: A86.1, CLA.11 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:P.10, A:P.11, A:Q.134 CLA.5: 19 residues within 4Å: Chain A: L.5, G.7, A.8, G.13, F.14, F.15, D.16, F.20, A.21, Y.32, R.33, V.35, E.36, R.137, M.140, L.141 Ligands: A86.1, ET4.2, CLA.6 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:F.15, A:F.20, A:E.36, A:R.137, A:M.140, A:L.141 Hydrogen bonds: A:A.8, A:F.15, A:R.137 Salt bridges: A:R.33 pi-Cation interactions: A:R.137, A:R.137 Metal complexes: A:E.36 CLA.6: 6 residues within 4Å: Chain A: R.31, V.35, H.39 Ligands: ET4.2, CLA.5, CLA.9 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:V.35 Salt bridges: A:R.31, A:R.31 pi-Stacking: A:H.39, A:H.39 CLA.7: 16 residues within 4Å: Chain A: F.42, L.45, A.46, G.49, P.53, F.66, V.76, W.83, L.84, T.87, V.90, I.91 Ligands: ET4.2, CLA.8, LHG.15, LMG.16 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:L.45, A:A.46, A:P.53, A:W.83, A:L.84, A:T.87, A:V.90, A:I.91 CLA.8: 18 residues within 4Å: Chain A: M.38, R.41, F.42, L.45, I.91, L.94, V.97, R.98, E.101, T.102, T.108, D.109, A.110 Ligands: CLA.7, CLA.10, LHG.15, LMG.16, LHG.18 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:I.91, A:R.98, A:E.101, A:E.101, A:T.102 Hydrogen bonds: A:R.41 CLA.9: 12 residues within 4Å: Chain A: V.35, M.38, H.39, F.42, I.91, S.92, E.95, T.96, R.98, L.99 Ligands: ET4.2, CLA.6 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:F.42, A:F.42, A:I.91, A:L.99, A:L.99 Hydrogen bonds: A:H.39 Salt bridges: A:R.98 Metal complexes: A:E.95 CLA.10: 18 residues within 4Å: Chain A: R.41, Q.44, T.108, D.109, A.110, I.112, W.117, R.118, P.119, Y.125, Y.128, Q.129, R.131, E.132 Ligands: A86.3, CLA.8, CLA.11, LHG.18 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:R.41, A:R.41, A:A.110, A:W.117, A:Y.125, A:Y.128, A:Q.129, A:R.131, A:E.132 Hydrogen bonds: A:D.109, A:A.110 Salt bridges: A:R.41 pi-Cation interactions: A:R.41, A:R.41 Metal complexes: A:E.132 CLA.11: 10 residues within 4Å: Chain A: L.48, Y.128, R.131, Q.135, L.138 Chain C: F.14 Ligands: A86.3, CLA.4, CLA.10, SQD.19 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:L.48, A:L.138 Salt bridges: A:R.131, A:R.131 CLA.12: 9 residues within 4Å: Chain A: L.141, G.145, A.148, Q.149, V.152, N.153, N.160 Ligands: A86.1, A86.3 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:L.141, A:A.148 Hydrogen bonds: A:Q.149, A:N.160 CLA.13: 4 residues within 4Å: Chain A: F.166, S.168 Ligands: SQD.19, CLA.49 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:F.166, A:F.166 Metal complexes: A:F.166 CLA.14: 3 residues within 4Å: Chain A: S.114, L.115 Ligands: A86.3 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:L.115, A:L.115 Metal complexes: A:L.115 CLA.25: 9 residues within 4Å: Chain B: I.8, P.10, L.120, Q.121, Q.124, H.125, L.128 Ligands: A86.21, CLA.31 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:I.8, B:P.10, B:P.10, B:Q.124, B:L.128 CLA.26: 20 residues within 4Å: Chain B: F.1, E.4, L.5, G.6, G.12, F.13, F.14, D.15, L.19, S.20, F.28, Y.31, R.32, E.35, H.38, R.127, M.130 Ligands: A86.21, DD6.23, CLA.37 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:F.14, B:F.14, B:F.28, B:Y.31, B:H.38, B:R.127, B:M.130 Hydrogen bonds: B:F.14, B:S.20 Salt bridges: B:R.32, B:R.127 pi-Cation interactions: B:R.127 Metal complexes: B:E.35 CLA.27: 17 residues within 4Å: Chain B: A.41, L.44, A.45, L.47, G.48, Y.55, R.56, F.57, F.59, I.61, T.67, I.70, I.80, W.85 Ligands: A86.22, DD6.23, CLA.36 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:L.44, B:A.45, B:L.47, B:Y.55, B:F.57, B:F.57, B:I.61, B:I.80, B:W.85 Hydrogen bonds: B:F.57, B:T.67 Salt bridges: B:R.56 CLA.28: 11 residues within 4Å: Chain B: I.61, A.62, P.63, P.81, L.83, G.84, Q.87, I.88, L.91 Chain C: N.78 Ligands: A86.22 2 PLIP interactions: 2 interactions with chain B, Hydrophobic interactions: B:I.61, B:L.91 CLA.29: 16 residues within 4Å: Chain B: A.34, K.37, H.38, I.89, F.90, I.92, G.93, D.96, Y.97 Chain C: F.90, V.97, R.98, W.100 Ligands: A86.22, CLA.37, CLA.46 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C, Hydrophobic interactions: B:K.37, B:F.90, B:I.92, B:Y.97, C:W.100 Salt bridges: B:K.37, C:R.98 pi-Cation interactions: B:K.37 Metal complexes: B:D.96 CLA.30: 15 residues within 4Å: Chain B: R.40, M.43, L.44, K.108, P.109, L.111, R.118, K.119, Q.121, E.122, H.125 Ligands: A86.22, DD6.24, CLA.31, CLA.33 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:R.40, B:M.43, B:L.44, B:P.109, B:L.111, B:R.118, B:K.119, B:Q.121 pi-Cation interactions: B:R.40, B:R.40 Metal complexes: B:E.122 CLA.31: 6 residues within 4Å: Chain B: Q.121, H.125, L.128 Ligands: DD6.24, CLA.25, CLA.30 3 PLIP interactions: 3 interactions with chain B, Hydrophobic interactions: B:L.128 pi-Stacking: B:H.125 Metal complexes: B:H.125 CLA.32: 7 residues within 4Å: Chain B: L.131, A.132, L.134, E.135, R.138 Ligands: A86.21, CLA.35 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:L.131, B:L.134, B:E.135 Hydrogen bonds: B:R.138 pi-Cation interactions: B:R.138, B:R.138, B:R.138 Metal complexes: B:E.135 CLA.33: 8 residues within 4Å: Chain B: L.91, V.95, L.101, G.102, F.104, G.107 Ligands: A86.22, CLA.30 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:L.91, B:V.95, B:L.101, B:L.101, B:F.104, B:F.104 Metal complexes: B:L.101 CLA.34: 7 residues within 4Å: Chain B: L.137, R.138, S.141, Q.142, V.145, F.149 Ligands: A86.21 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:L.137, B:R.138, B:V.145, B:F.149 CLA.35: 7 residues within 4Å: Chain B: T.157, G.158, L.159, P.160, F.161 Ligands: DD6.24, CLA.32 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:L.159, B:P.160, B:F.161, B:F.161 Metal complexes: B:G.158 CLA.36: 9 residues within 4Å: Chain B: L.47, I.50, A.51, T.54, Y.55, L.159, F.161, M.162 Ligands: CLA.27 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:L.47, B:A.51, B:Y.55, B:Y.55, B:L.159, B:F.161 CLA.37: 7 residues within 4Å: Chain B: Y.31, H.38 Chain C: F.90, R.98 Ligands: DD6.23, CLA.26, CLA.29 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C, pi-Stacking: B:H.38 Metal complexes: B:H.38 Hydrophobic interactions: C:F.90, C:F.90 Salt bridges: C:R.98 CLA.41: 10 residues within 4Å: Chain C: I.8, A.9, P.10, L.120, Q.121, Q.124, H.125, L.128 Ligands: A86.20, CLA.48 4 PLIP interactions: 4 interactions with chain C, Hydrophobic interactions: C:I.8, C:I.8, C:Q.124, C:L.128 CLA.42: 21 residues within 4Å: Chain C: F.1, E.4, L.5, G.6, V.7, T.11, G.12, F.13, F.14, D.15, F.19, T.20, F.28, Y.31, R.32, E.35, R.127, M.130 Ligands: A86.20, DD6.39, CLA.43 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:F.14, C:F.28, C:Y.31, C:R.127 Hydrogen bonds: C:F.14, C:D.15, C:D.15, C:R.127 Salt bridges: C:R.32 pi-Cation interactions: C:R.127, C:R.127 Metal complexes: C:E.35 CLA.43: 9 residues within 4Å: Chain B: F.90, W.98 Chain C: Q.30, Y.31, A.34, H.38 Ligands: DD6.39, CLA.42, CLA.46 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B, Hydrophobic interactions: C:A.34, B:F.90, B:F.90 Hydrogen bonds: C:Q.30 pi-Stacking: C:H.38 Metal complexes: C:H.38 CLA.44: 17 residues within 4Å: Chain C: V.41, L.44, A.45, V.47, G.48, P.52, F.55, R.56, W.57, F.59, C.67, V.70, P.71, I.80, W.85 Ligands: A86.38, DD6.39 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:L.44, C:A.45, C:P.52, C:W.57, C:I.80, C:W.85 Hydrogen bonds: C:W.57 CLA.45: 9 residues within 4Å: Chain C: A.62, P.63, P.81, L.83, G.84, Q.87, I.88, A.91 Ligands: A86.38 4 PLIP interactions: 4 interactions with chain C, Hydrophobic interactions: C:P.63, C:I.88, C:A.91 Hydrogen bonds: C:A.62 CLA.46: 18 residues within 4Å: Chain B: A.86, Q.87, F.90, Y.97, W.98 Chain C: T.33, A.34, K.37, H.38, V.41, I.89, F.90, I.92, G.93, D.96 Ligands: CLA.29, A86.38, CLA.43 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain C, Hydrophobic interactions: B:Q.87, B:F.90, B:F.90, B:F.90, B:Y.97, C:K.37, C:V.41, C:I.89, C:I.92 pi-Stacking: B:F.90 Salt bridges: C:K.37 pi-Cation interactions: C:K.37 Metal complexes: C:D.96 CLA.47: 15 residues within 4Å: Chain C: R.40, Q.43, L.44, G.107, K.108, P.109, L.111, R.118, A.119, E.122, H.125 Ligands: A86.38, DD6.40, CLA.48, CLA.50 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:R.40, C:R.40, C:Q.43, C:L.44, C:L.111, C:R.118 pi-Cation interactions: C:R.40, C:R.40 Metal complexes: C:E.122 CLA.48: 6 residues within 4Å: Chain C: Q.121, H.125, L.128 Ligands: DD6.40, CLA.41, CLA.47 4 PLIP interactions: 4 interactions with chain C, Hydrophobic interactions: C:L.128 pi-Stacking: C:H.125, C:H.125 Metal complexes: C:H.125 CLA.49: 10 residues within 4Å: Chain C: L.131, A.132, E.135, R.138, L.152 Ligands: CLA.13, SQD.19, A86.20, CLA.51, CLA.52 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:L.131, C:A.132, C:E.135 Salt bridges: C:R.138 pi-Cation interactions: C:R.138, C:R.138 Metal complexes: C:E.135 CLA.50: 9 residues within 4Å: Chain C: V.95, F.101, G.102, F.104, I.106, G.107 Ligands: A86.38, DD6.40, CLA.47 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:V.95, C:F.101, C:F.104, C:F.104 pi-Stacking: C:F.104 Metal complexes: C:F.101 CLA.51: 8 residues within 4Å: Chain C: L.137, R.138, S.141, Q.142, V.145, F.149 Ligands: A86.20, CLA.49 5 PLIP interactions: 5 interactions with chain C, Hydrophobic interactions: C:L.137, C:R.138, C:V.145, C:F.149, C:F.149 CLA.52: 6 residues within 4Å: Chain C: T.157, G.158, L.159, P.160 Ligands: DD6.40, CLA.49 3 PLIP interactions: 3 interactions with chain C, Hydrophobic interactions: C:L.159, C:P.160 Metal complexes: C:G.158

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

LHG.15: 3 residues within 4Å: Ligands: CLA.7, CLA.8, LHG.18 No protein-ligand interaction detected (PLIP) LHG.17: 2 residues within 4Å: Chain A: D.80, L.82 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.82 Hydrogen bonds: A:D.80 LHG.18: 8 residues within 4Å: Chain A: E.101, A.110, K.111, I.112 Ligands: A86.3, CLA.8, CLA.10, LHG.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.112 Hydrogen bonds: A:E.101 Salt bridges: A:K.111

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

LMG.16: 5 residues within 4Å: Chain A: G.60, S.61, F.62 Ligands: CLA.7, CLA.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.62

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

SQD.19: 11 residues within 4Å: Chain A: K.55, L.158, W.169 Chain C: R.138, Q.142, F.149, D.150 Ligands: CLA.11, CLA.13, A86.20, CLA.49 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:R.138, C:F.149 Hydrophobic interactions: A:L.158 Salt bridges: A:K.55, A:K.55

4 x DD6: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol(Non-covalent)

DD6.23: 14 residues within 4Å: Chain B: F.14, D.15, P.16, L.17, A.45, Y.49, G.73, M.130, L.131, F.133, L.134 Ligands: CLA.26, CLA.27, CLA.37 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.14, B:A.45, B:M.130, B:L.131, B:F.133, B:F.133, B:F.133, B:F.133, B:L.134 Hydrogen bonds: B:F.14, B:L.17, B:G.73, B:G.73 DD6.24: 17 residues within 4Å: Chain B: M.43, V.46, L.47, I.50, G.107, H.125, L.128, A.129, A.132, L.136, I.156, T.157, G.158, L.159 Ligands: CLA.30, CLA.31, CLA.35 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:M.43, B:V.46, B:L.47, B:I.50, B:L.128, B:A.129, B:A.132, B:L.136, B:I.156, B:L.159 Hydrogen bonds: B:G.158 DD6.39: 17 residues within 4Å: Chain C: F.14, D.15, P.16, L.17, F.19, V.41, A.45, Y.49, N.72, G.73, I.77, M.130, I.133, L.134 Ligands: CLA.42, CLA.43, CLA.44 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.14, C:F.19, C:V.41, C:A.45, C:Y.49, C:I.133, C:I.133, C:L.134 Hydrogen bonds: C:D.15, C:L.17, C:G.73 DD6.40: 13 residues within 4Å: Chain C: Q.43, V.46, I.106, G.107, A.132, L.136, I.156, T.157, G.158 Ligands: CLA.47, CLA.48, CLA.50, CLA.52 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Q.43, C:A.132, C:L.136, C:L.136, C:I.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, S. et al., Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana. Nat Commun (2023)

Release Date

2023-12-20

Peptides

FCPII-G, Fucoxanthin chlorophyll a/c binding protein: A
FCPII-H2, Fucoxanthin chlorophyll a/c binding protein: B
FCPII-H1, Fucoxanthin chlorophyll a/c binding protein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
5

B
7

C
6

Membrane

We predict this structure to be a membrane protein.
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FCPII-G, Fucoxanthin chlorophyll a/c binding protein

FCPII-H2, Fucoxanthin chlorophyll a/c binding protein

FCPII-H1, Fucoxanthin chlorophyll a/c binding protein

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