SMTL ID : 8w4p.1

Structure of PSII-FCPII-I/J/K complex in the PSII-FCPII supercomplex from Cyclotella meneghiniana

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

30 x CLA: CHLOROPHYLL A(Non-covalent)(Non-functional Binders)

CLA.1: 6 residues within 4Å: Chain A: P.2, R.3, L.5, V.22, F.24 Ligands: CLA.2 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:L.5, A:V.22 Metal complexes: A:R.3 CLA.2: 13 residues within 4Å: Chain A: G.20, D.21, V.22, G.23, F.24, L.51, L.54, R.55, E.58, H.61, R.172, M.175 Ligands: CLA.1 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:F.24, A:L.54, A:L.54, A:L.54, A:L.54, A:E.58, A:H.61, A:R.172, A:M.175 Hydrogen bonds: A:V.22, A:G.23, A:F.24 CLA.3: 2 residues within 4Å: Chain A: H.61 Ligands: DD6.11 3 PLIP interactions: 3 interactions with chain A, pi-Stacking: A:H.61 pi-Cation interactions: A:H.61 Metal complexes: A:H.61 CLA.4: 9 residues within 4Å: Chain A: I.64, L.67, A.68, L.70, G.71, W.74, P.82, G.83 Ligands: DD6.11 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:A.68, A:L.70, A:W.74 CLA.5: 7 residues within 4Å: Chain A: W.53, A.57, T.60, H.61, M.117, A.118, E.121 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:W.53, A:W.53, A:T.60, A:M.117, A:A.118, A:E.121 CLA.6: 9 residues within 4Å: Chain A: R.63, D.139, L.142, Y.160, K.163, Q.164, Q.166, E.167 Ligands: A86.10 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:R.63, A:D.139, A:L.142, A:Y.160, A:Y.160, A:Q.164, A:E.167, A:E.167 CLA.7: 5 residues within 4Å: Chain A: Q.166, K.169, H.170, L.173 Ligands: CLA.8 2 PLIP interactions: 2 interactions with chain A, Hydrophobic interactions: A:K.169, A:L.173 CLA.8: 5 residues within 4Å: Chain A: Q.166, H.170, L.173 Ligands: CLA.7, A86.10 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:L.173 pi-Stacking: A:H.170, A:H.170 Metal complexes: A:H.170 CLA.9: 7 residues within 4Å: Chain A: I.176, F.179, G.180, F.183, Q.184, N.187 Ligands: A86.10 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:I.176, A:F.179, A:F.183 Hydrogen bonds: A:N.187 CLA.15: 5 residues within 4Å: Chain B: X.5, X.131, X.132, X.135 Ligands: CLA.22 0 PLIP interactions: CLA.16: 8 residues within 4Å: Chain B: X.7, X.25, X.26, X.28, X.29, X.138, X.141 Ligands: A86.13 0 PLIP interactions: CLA.17: 2 residues within 4Å: Ligands: A86.13, CLA.20 0 PLIP interactions: CLA.18: 11 residues within 4Å: Chain B: X.35, X.38, X.41, X.45, X.50, X.51, X.52, X.53 Ligands: A86.12, A86.13, CLA.24 0 PLIP interactions: CLA.19: 9 residues within 4Å: Chain B: X.56, X.57, X.77, X.79, X.80, X.83, X.84, X.87 Ligands: A86.12 0 PLIP interactions: CLA.20: 5 residues within 4Å: Chain B: X.35, X.85, X.89 Ligands: A86.12, CLA.17 0 PLIP interactions: CLA.21: 9 residues within 4Å: Chain B: X.34, X.108, X.109, X.110, X.129, X.133 Ligands: A86.12, A86.14, CLA.22 0 PLIP interactions: CLA.22: 4 residues within 4Å: Chain B: X.132 Ligands: A86.14, CLA.15, CLA.21 0 PLIP interactions: CLA.23: 3 residues within 4Å: Chain B: X.146, X.150 Ligands: A86.14 0 PLIP interactions: CLA.24: 7 residues within 4Å: Chain B: X.72, X.73, X.74, X.76 Ligands: A86.13, CLA.18, A86.25 0 PLIP interactions: CLA.28: 5 residues within 4Å: Chain C: A.8, S.121, Q.124, H.125 Ligands: A86.25 1 PLIP interactions: 1 interactions with chain C, Hydrophobic interactions: C:Q.124 CLA.29: 12 residues within 4Å: Chain C: G.5, F.12, F.13, Y.30, R.31, A.33, E.34, H.37, R.127, M.130 Ligands: A86.25, DD6.27 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:F.13, C:Y.30, C:A.33, C:E.34, C:H.37, C:M.130 Hydrogen bonds: C:F.13 Salt bridges: C:R.31 pi-Cation interactions: C:R.127, C:R.127, C:R.127 CLA.30: 2 residues within 4Å: Chain C: H.37 Ligands: DD6.27 2 PLIP interactions: 2 interactions with chain C, pi-Cation interactions: C:H.37 Metal complexes: C:H.37 CLA.31: 13 residues within 4Å: Chain C: A.40, L.43, A.44, L.46, G.47, A.50, P.51, R.55, F.56, T.67, A.76 Ligands: DD6.27, CLA.38 5 PLIP interactions: 5 interactions with chain C, Hydrophobic interactions: C:L.43, C:L.46, C:A.50, C:A.76 Hydrogen bonds: C:F.56 CLA.32: 6 residues within 4Å: Chain C: L.32, A.33, K.36, H.37, V.92, G.93 3 PLIP interactions: 3 interactions with chain C, Hydrophobic interactions: C:K.36, C:V.92 pi-Cation interactions: C:K.36 CLA.33: 10 residues within 4Å: Chain C: R.39, M.42, L.43, V.107, R.118, Q.119, S.121, E.122, H.125 Ligands: A86.26 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:R.39, C:R.39, C:M.42, C:L.43, C:R.118, C:E.122, C:H.125 pi-Cation interactions: C:R.39 CLA.34: 2 residues within 4Å: Chain C: H.125 Ligands: A86.26 2 PLIP interactions: 2 interactions with chain C, pi-Stacking: C:H.125 Metal complexes: C:H.125 CLA.35: 7 residues within 4Å: Chain C: L.131, L.134, E.135, R.138 Ligands: A86.25, CLA.36, CLA.37 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:L.134, C:E.135 Salt bridges: C:R.138 pi-Cation interactions: C:R.138, C:R.138, C:R.138 Metal complexes: C:E.135 CLA.36: 7 residues within 4Å: Chain C: I.137, R.138, S.141, Q.142, A.145 Ligands: A86.25, CLA.35 2 PLIP interactions: 2 interactions with chain C, Hydrophobic interactions: C:I.137, C:R.138 CLA.37: 6 residues within 4Å: Chain C: T.157, G.158, L.159, P.160 Ligands: A86.26, CLA.35 3 PLIP interactions: 3 interactions with chain C, Hydrophobic interactions: C:T.157, C:L.159, C:P.160 CLA.38: 8 residues within 4Å: Chain C: L.46, V.49, A.50, T.53, Y.54, F.161, L.162 Ligands: CLA.31 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:L.46, C:A.50, C:T.53, C:Y.54, C:F.161, C:L.162

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)

A86.10: 14 residues within 4Å: Chain A: Q.66, G.143, N.149, P.150, H.170, L.173, A.174, L.181, Q.184, I.192, L.196 Ligands: CLA.6, CLA.8, CLA.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.66, A:N.149, A:L.173, A:A.174 Hydrogen bonds: A:Q.184 A86.12: 7 residues within 4Å: Chain B: X.55, X.56, X.96 Ligands: CLA.18, CLA.19, CLA.20, CLA.21 No protein-ligand interaction detected (PLIP) A86.13: 11 residues within 4Å: Chain B: X.10, X.39, X.42, X.68, X.69, X.70, X.141 Ligands: CLA.16, CLA.17, CLA.18, CLA.24 No protein-ligand interaction detected (PLIP) A86.14: 9 residues within 4Å: Chain B: X.37, X.40, X.136, X.139, X.140, X.143 Ligands: CLA.21, CLA.22, CLA.23 No protein-ligand interaction detected (PLIP) A86.25: 7 residues within 4Å: Chain C: P.9, L.128 Ligands: CLA.24, CLA.28, CLA.29, CLA.35, CLA.36 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.9 A86.26: 15 residues within 4Å: Chain C: M.42, L.46, S.103, G.106, H.125, A.132, E.135, L.136, I.156, T.157, G.158, L.159 Ligands: CLA.33, CLA.34, CLA.37 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:M.42, C:L.46, C:A.132, C:E.135, C:L.136, C:L.136, C:L.159 Hydrogen bonds: C:G.158, C:G.158

2 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)

DD6.11: 10 residues within 4Å: Chain A: F.24, P.26, I.27, G.28, G.71, F.72, P.98, M.175 Ligands: CLA.3, CLA.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.24, A:F.72, A:F.72, A:M.175, A:M.175 Hydrogen bonds: A:I.27, A:G.28, A:P.98 DD6.27: 15 residues within 4Å: Chain C: F.13, D.14, P.15, A.16, L.18, H.37, A.44, Y.48, G.73, A.76, M.130, F.133 Ligands: CLA.29, CLA.30, CLA.31 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.18, C:Y.48, C:M.130, C:M.130, C:F.133, C:F.133, C:F.133, C:F.133 Hydrogen bonds: C:D.14, C:G.73, C:G.73

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-I, Fucoxanthin chlorophyll a/c binding protein: A
FCPII-K, Fucoxanthin chlorophyll a/c binding protein: B
FCPII-J, Fucoxanthin chlorophyll a/c binding protein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
p

B
4

C
3

Membrane

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

FCPII-K, Fucoxanthin chlorophyll a/c binding protein

FCPII-J, Fucoxanthin chlorophyll a/c binding protein

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