› 7vd5

Electron Microscopy
2.5Å resolution

Structure of C2S2M2-type PSII-FCPII supercomplex from diatom

Released:
DOI: 10.2210/pdb7vd5/pdb
PDB entry 7vd5 coloured by chain, front view.
PDB entry 7vd5 coloured by chain, side view.
PDB entry 7vd5 coloured by chain, top view.
Source organism: Chaetoceros gracilis
Primary publication:
Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex
Nagao R, Kato K, Kumazawa M, Ifuku K, Yokono M, Suzuki T, Dohmae N, Akita F, Akimoto S, Miyazaki N, Shen JR
Nat Commun 13 1764- (2022)
Related structures: EMD-31905

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 68-mer (preferred)
PDBe Complex ID:
PDB-CPX-105521 (preferred)
Entry contents:
34 distinct polypeptide molecules
Macromolecules (34 distinct):
Photosystem II protein D1 Chains: A, a
Molecule details ›
Chains: A, a
Length: 334 amino acids
Theoretical weight: 37.04 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679C261 (Residues: 11-344; 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: 484 amino acids
Theoretical weight: 53.76 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679C6E3 (Residues: 2-485; 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: 451 amino acids
Theoretical weight: 49.47 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679BVV7 (Residues: 21-471; Coverage: 96%)
Gene name: psbC
Sequence domains: Photosystem II protein
Photosystem II D2 protein Chains: D, d
Molecule details ›
Chains: D, d
Length: 341 amino acids
Theoretical weight: 37.98 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679C012 (Residues: 11-351; 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: Chaetoceros gracilis
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: 28 amino acids
Theoretical weight: 3.21 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679BVT0 (Residues: 16-43; Coverage: 65%)
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: 66 amino acids
Theoretical weight: 7.29 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: B7XBY7 (Residues: 2-67; Coverage: 99%)
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: 35 amino acids
Theoretical weight: 4.07 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679BVT8 (Residues: 1-35; Coverage: 92%)
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: 3.59 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679C298 (Residues: 6-39; 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: 4.22 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679BWI3 (Residues: 8-44; Coverage: 84%)
Gene name: psbK
Sequence domains: Photosystem II 4 kDa reaction centre component
Photosystem II reaction center protein L Chains: L, l
Molecule details ›
Chains: L, l
Length: 38 amino acids
Theoretical weight: 4.37 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679C262 (Residues: 1-38; Coverage: 100%)
Gene name: psbL
Sequence domains: PsbL protein
Photosystem II subunit Chains: M, m
Molecule details ›
Chains: M, m
Length: 42 amino acids
Theoretical weight: 4.47 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679C2A0 (Residues: 44-85; Coverage: 32%)
Gene name: psbM
Extrinsic protein in photosystem II Chains: O, o
Molecule details ›
Chains: O, o
Length: 245 amino acids
Theoretical weight: 26.42 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: B6ZHE8 (Residues: 62-306; Coverage: 84%)
Gene name: psbO
Sequence domains: Manganese-stabilising protein / photosystem II polypeptide
Photosystem II reaction center protein T Chains: T, t
Molecule details ›
Chains: T, t
Length: 30 amino acids
Theoretical weight: 3.55 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679C6E6 (Residues: 1-30; Coverage: 97%)
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: 93 amino acids
Theoretical weight: 10.14 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: B6ZHF0 (Residues: 59-151; 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: 14.78 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: B6ZHF4 (Residues: 28-163; Coverage: 83%)
Gene name: psbV
Sequence domains: Cytochrome c-550 domain
Photosystem II reaction center protein Ycf12 Chains: Y, y
Molecule details ›
Chains: Y, y
Length: 34 amino acids
Theoretical weight: 3.61 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679BVT2 (Residues: 1-34; Coverage: 100%)
Gene name: ycf12
Sequence domains: Photosystem II complex subunit Ycf12
Photosystem II reaction center protein X Chains: X, x
Molecule details ›
Chains: X, x
Length: 37 amino acids
Theoretical weight: 3.77 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: B6ZHF2 (Residues: 1-37; Coverage: 97%)
Gene name: psbX
Sequence domains: Photosystem II reaction centre X protein (PsbX)
Photosystem II reaction center protein Z Chains: Z, z
Molecule details ›
Chains: Z, z
Length: 59 amino acids
Theoretical weight: 6.33 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679C215 (Residues: 1-59; Coverage: 95%)
Gene name: psbZ
Sequence domains: YCF9
Extrinsic protein in photosystem II Chains: Q, q
Molecule details ›
Chains: Q, q
Length: 151 amino acids
Theoretical weight: 16.73 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: B6ZHE9 (Residues: 61-211; Coverage: 77%)
Gene name: psbQ'
Photosystem II reaction center protein W Chains: W, w
Molecule details ›
Chains: W, w
Length: 52 amino acids
Theoretical weight: 5.94 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679C6E8 (Residues: 32-83; Coverage: 62%)
Gene name: psbW
Unknown protein 0 Chains: 0, 5
Molecule details ›
Chains: 0, 5
Length: 31 amino acids
Theoretical weight: 2.66 KDa
Source organism: Chaetoceros gracilis
Unknown protein 1 Chains: 1, 6
Molecule details ›
Chains: 1, 6
Length: 30 amino acids
Theoretical weight: 2.57 KDa
Source organism: Chaetoceros gracilis
Chlorophyll a/b-binding protein Chains: 11, 31
Molecule details ›
Chains: 11, 31
Length: 176 amino acids
Theoretical weight: 19.11 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679BXP6 (Residues: 31-206; Coverage: 92%)
Gene name: lhcf1
Sequence domains: Chlorophyll A-B binding protein
Fcpb2, Fucoxanthin chlorophyll a/c-binding protein Chains: 12, 32
Molecule details ›
Chains: 12, 32
Length: 169 amino acids
Theoretical weight: 18.53 KDa
Source organism: Chaetoceros gracilis
Chlorophyll a/b-binding protein Chains: 13, 33
Molecule details ›
Chains: 13, 33
Length: 169 amino acids
Theoretical weight: 18.45 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679BXP6 (Residues: 31-199; Coverage: 88%)
Gene name: lhcf1
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a/b-binding protein Chains: 14, 34
Molecule details ›
Chains: 14, 34
Length: 172 amino acids
Theoretical weight: 18.77 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679BXP6 (Residues: 31-202; Coverage: 90%)
Gene name: lhcf1
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a/b-binding protein Chains: 15, 35
Molecule details ›
Chains: 15, 35
Length: 170 amino acids
Theoretical weight: 18.6 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679BXP6 (Residues: 31-200; Coverage: 89%)
Gene name: lhcf1
Sequence domains: Chlorophyll A-B binding protein
Fcpb3, Fucoxanthin chlorophyll a/c-binding protein Chains: 16, 36
Molecule details ›
Chains: 16, 36
Length: 179 amino acids
Theoretical weight: 19.62 KDa
Source organism: Chaetoceros gracilis
Fcpb4, Fucoxanthin chlorophyll a/c-binding protein Chains: 17, 37
Molecule details ›
Chains: 17, 37
Length: 176 amino acids
Theoretical weight: 19.2 KDa
Source organism: Chaetoceros gracilis
Chlorophyll a/b-binding protein Chains: 18, 38
Molecule details ›
Chains: 18, 38
Length: 168 amino acids
Theoretical weight: 18.35 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A679BXP6 (Residues: 31-198; Coverage: 88%)
Gene name: lhcf1
Sequence domains: Chlorophyll A-B binding protein
Fcpb5, Fucoxanthin chlorophyll a/c-binding protein Chains: 19, 39
Molecule details ›
Chains: 19, 39
Length: 227 amino acids
Theoretical weight: 24.68 KDa
Source organism: Chaetoceros gracilis
Fcpb6, Fucoxanthin chlorophyll a/c-binding protein Chains: 20, 40
Molecule details ›
Chains: 20, 40
Length: 155 amino acids
Theoretical weight: 16.97 KDa
Source organism: Chaetoceros gracilis
Fcpb7, Fucoxanthin chlorophyll a/c-binding protein Chains: 21, 41
Molecule details ›
Chains: 21, 41
Length: 162 amino acids
Theoretical weight: 17.89 KDa
Source organism: Chaetoceros gracilis

Ligands and Environments


Cofactor: Ligand HEM 4 x HEM
16 bound ligands:
Ligand OEX 2 x OEX
Ligand FE2 2 x FE2
Ligand CLA 220 x CLA
Ligand PHO 4 x PHO
Ligand BCR 24 x BCR
Ligand SQD 10 x SQD
Ligand LMG 22 x LMG
Ligand BCT 2 x BCT
Ligand LHG 16 x LHG
Ligand DGD 8 x DGD
Ligand PL9 4 x PL9
Ligand KC1 70 x KC1
Ligand A86 108 x A86
Ligand UNL 38 x UNL
Ligand DD6 12 x DD6
Ligand LMU 2 x LMU
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.5Å
Relevant EMDB volumes: EMD-31905

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