› 8j5k

Electron Microscopy
2.93Å resolution

Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana

Released:
DOI: 10.2210/pdb8j5k/pdb
PDB entry 8j5k coloured by chain, front view.
PDB entry 8j5k coloured by chain, side view.
PDB entry 8j5k coloured by chain, top view.
Source organism: Stephanocyclus meneghinianus
Primary publication:
Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana.
Zhao S, Shen L, Li X, Tao Q, Li Z, Xu C, Zhou C, Yang Y, Sang M, Han G, Yu LJ, Kuang T, Shen JR, Wang W
Nat Commun 14 8164 (2023)
PMID: 38071196
Related structures: EMD-35987

Function and Biology Details

Reaction catalysed: 
2 H(2)O + 2 plastoquinone + 4 light = O(2) + 2 plastoquinol
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 56-mer (preferred)
PDBe Complex ID:
PDB-CPX-242080 (preferred)
Entry contents:
28 distinct polypeptide molecules
Macromolecules (28 distinct):
Photosystem II protein D1 Chains: A, a
Molecule details ›
Chains: A, a
Length: 333 amino acids
Theoretical weight: 36.95 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: A0A8F5GJ32 (Residues: 11-343; Coverage: 93%)
Gene name: psbA
Sequence domains: Photosynthetic reaction centre protein
Photosystem II CP47 reaction center protein Chains: B, b
Molecule details ›
Chains: B, b
Length: 481 amino acids
Theoretical weight: 53.5 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: A0A679C6E3 (Residues: 2-482; Coverage: 95%)
Gene name: psbB
Sequence domains: Photosystem II protein
Photosystem II CP43 reaction center protein Chains: C, c
Molecule details ›
Chains: C, c
Length: 450 amino acids
Theoretical weight: 49.36 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: A0A8F5GHI6 (Residues: 21-470; Coverage: 96%)
Gene name: psbC
Sequence domains: Photosystem II protein
Photosystem II D2 protein Chains: D, d
Molecule details ›
Chains: D, d
Length: 340 amino acids
Theoretical weight: 37.83 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: A0A679C012 (Residues: 12-351; Coverage: 97%)
Gene name: psbD
Sequence domains: Photosynthetic reaction centre protein
Cytochrome b559 subunit alpha Chains: E, e
Molecule details ›
Chains: E, e
Length: 75 amino acids
Theoretical weight: 8.69 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: A0A679C209 (Residues: 9-83; Coverage: 89%)
Gene name: psbE
Sequence domains:
Cytochrome b559 subunit beta Chains: F, f
Molecule details ›
Chains: F, f
Length: 31 amino acids
Theoretical weight: 3.56 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: A0T0U1 (Residues: 13-43; Coverage: 72%)
Gene name: psbF
Sequence domains: Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits
Photosystem II reaction center protein H Chains: H, h
Molecule details ›
Chains: H, h
Length: 65 amino acids
Theoretical weight: 7.19 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: B7XBY7 (Residues: 2-66; Coverage: 97%)
Gene name: psbH
Sequence domains: Photosystem II 10 kDa phosphoprotein
Photosystem II reaction center protein I Chains: I, i
Molecule details ›
Chains: I, i
Length: 34 amino acids
Theoretical weight: 3.94 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: A0A679BVT8 (Residues: 1-34; Coverage: 90%)
Gene name: psbI
Sequence domains: Photosystem II reaction centre I protein (PSII 4.8 kDa protein)
Photosystem II reaction center protein J Chains: J, j
Molecule details ›
Chains: J, j
Length: 34 amino acids
Theoretical weight: 3.49 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: A0T0T9 (Residues: 5-38; Coverage: 87%)
Gene name: psbJ
Sequence domains: PsbJ
Photosystem II reaction center protein K Chains: K, k
Molecule details ›
Chains: K, k
Length: 37 amino acids
Theoretical weight: 4.23 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: A0A2H5N031 (Residues: 18-54; Coverage: 69%)
Gene name: CUMW_285680
Sequence domains: Photosystem II 4 kDa reaction centre component
Photosystem II reaction center L Chains: L, l
Molecule details ›
Chains: L, l
Length: 37 amino acids
Theoretical weight: 4.24 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: A0A151DYG7 (Residues: 2-38; Coverage: 97%)
Gene names: AYK24_09260, psbL
Sequence domains: PsbL protein
Photosystem II subunit Chains: M, m
Molecule details ›
Chains: M, m
Length: 41 amino acids
Theoretical weight: 4.36 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: A0A679C2A0 (Residues: 44-84; Coverage: 31%)
Gene name: psbM
Psb34 Chains: N, n
Molecule details ›
Chains: N, n
Length: 30 amino acids
Theoretical weight: 2.57 KDa
Source organism: Stephanocyclus meneghinianus
Extrinsic protein in photosystem II Chains: O, o
Molecule details ›
Chains: O, o
Length: 248 amino acids
Theoretical weight: 26.75 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: B6ZHE8 (Residues: 60-307; Coverage: 85%)
Gene name: psbO
Sequence domains: Manganese-stabilising protein / photosystem II polypeptide
Extrinsic protein in photosystem II Chains: Q, q
Molecule details ›
Chains: Q, q
Length: 145 amino acids
Theoretical weight: 16 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: B6ZHE9 (Residues: 65-209; Coverage: 74%)
Gene name: psbQ'
Photosystem II reaction center protein T Chains: T, t
Molecule details ›
Chains: T, t
Length: 29 amino acids
Theoretical weight: 3.44 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: A0A679C6E6 (Residues: 1-29; Coverage: 94%)
Gene name: psbT
Sequence domains: Photosystem II reaction centre T protein
Photosystem II 12 kDa extrinsic protein Chains: U, u
Molecule details ›
Chains: U, u
Length: 92 amino acids
Theoretical weight: 10.01 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: B6ZHF0 (Residues: 59-150; Coverage: 68%)
Gene name: psbU
Sequence domains: Photosystem II 12 kDa extrinsic protein (PsbU)
Photosystem II extrinsic protein V Chains: V, v
Molecule details ›
Chains: V, v
Length: 136 amino acids
Theoretical weight: 14.76 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: A0A8F5GGT9 (Residues: 27-162; Coverage: 83%)
Gene name: psbV
Sequence domains: Cytochrome c-550 domain
PsbW Chains: W, w
Molecule details ›
Chains: W, w
Length: 50 amino acids
Theoretical weight: 5.61 KDa
Source organism: Stephanocyclus meneghinianus
Photosystem II reaction center protein X Chains: X, x
Molecule details ›
Chains: X, x
Length: 34 amino acids
Theoretical weight: 3.39 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: B6ZHF2 (Residues: 1-34; Coverage: 90%)
Gene name: psbX
Sequence domains: Photosystem II reaction centre X protein (PsbX)
Photosystem II reaction center protein Y Chains: Y, y
Molecule details ›
Chains: Y, y
Length: 33 amino acids
Theoretical weight: 3.63 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: A0T0V3 (Residues: 2-34; Coverage: 92%)
Gene names: psbY-A, psbY-B
Sequence domains: Photosystem II protein Y (PsbY)
Photosystem II reaction center protein Z Chains: Z, z
Molecule details ›
Chains: Z, z
Length: 59 amino acids
Theoretical weight: 6.23 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: A0T0T3 (Residues: 1-59; Coverage: 94%)
Gene names: THAPSDRAFT_bd1426, psbZ
Sequence domains: YCF9
FCPII-G, fucoxanthin chlorophyll a/c binding protein Chains: 0, 5
Molecule details ›
Chains: 0, 5
Length: 169 amino acids
Theoretical weight: 18.51 KDa
Source organism: Stephanocyclus meneghinianus
FCPII-H2, fucoxanthin chlorophyll a/c binding protein Chains: 2, 7
Molecule details ›
Chains: 2, 7
Length: 164 amino acids
Theoretical weight: 18.25 KDa
Source organism: Stephanocyclus meneghinianus
Fucoxanthin chlorophyll a/c light-harvesting protein, major type Chains: 1, 6
Molecule details ›
Chains: 1, 6
Length: 164 amino acids
Theoretical weight: 18.09 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: B8BX93 (Residues: 31-194; Coverage: 92%)
Gene names: Lhcf7, THAPSDRAFT_21667
Sequence domains: Chlorophyll A-B binding protein
Fucoxanthin chl a/c protein, lhca clade Chains: P, p
Molecule details ›
Chains: P, p
Length: 214 amino acids
Theoretical weight: 23.28 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: B8BUU4 (Residues: 34-247; Coverage: 91%)
Gene names: Lhca2, THAPSDRAFT_2601
Sequence domains: Chlorophyll A-B binding protein
FCPII-K, fucoxanthin chlorophyll a/c binding protein Chains: 4, 9
Molecule details ›
Chains: 4, 9
Length: 153 amino acids
Theoretical weight: 13.04 KDa
Source organism: Stephanocyclus meneghinianus
Fucoxanthin-chlorophyll a-c binding protein, plastid Chains: 3, 8
Molecule details ›
Chains: 3, 8
Length: 163 amino acids
Theoretical weight: 17.85 KDa
Source organism: Stephanocyclus meneghinianus
UniProt:
  • Canonical: B8BVI1 (Residues: 33-195; Coverage: 91%)
Gene names: Lhcf11, THAPSDRAFT_270241
Sequence domains: Chlorophyll A-B binding protein

Ligands and Environments


Cofactor: Ligand HEM 4 x HEM
15 bound ligands:
Ligand OEX 2 x OEX
Ligand FE2 2 x FE2
Ligand CLA 206 x CLA
Ligand PHO 4 x PHO
Ligand BCR 20 x BCR
Ligand SQD 8 x SQD
Ligand PL9 4 x PL9
Ligand LHG 14 x LHG
Ligand LMG 22 x LMG
Ligand CL 2 x CL
Ligand DGD 8 x DGD
Ligand BCT 2 x BCT
Ligand A86 24 x A86
Ligand ET4 2 x ET4
Ligand DD6 12 x DD6
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.93Å
Relevant EMDB volumes: EMD-35987

Quick links