› 7pnk

Electron Microscopy
3.61Å resolution

Unstacked compact Dunaliella PSII

Released:
DOI: 10.2210/pdb7pnk/pdb
PDB entry 7pnk coloured by chain, front view.
PDB entry 7pnk coloured by chain, side view.
PDB entry 7pnk coloured by chain, top view.
Source organism: Dunaliella salina
Primary publication:
Structure of Dunaliella Photosystem II reveals conformational flexibility of stacked and unstacked supercomplexes.
Caspy I, Fadeeva M, Mazor Y, Nelson N
OpenAccess logo Elife 12 (2023)
PMID: 36799903
Related structures: EMD-13548

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 44-mer (preferred)
PDBe Complex ID:
PDB-CPX-103332 (preferred)
Entry contents:
24 distinct polypeptide molecules
Macromolecules (24 distinct):
Photosystem II protein D1 Chains: A, a
Molecule details ›
Chains: A, a
Length: 336 amino acids
Theoretical weight: 37.29 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: D0FY08 (Residues: 9-344; Coverage: 95%)
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: 53.32 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: A0A1C8XRM6 (Residues: 2-485; Coverage: 95%)
Gene name: psbB
Sequence domains: Photosystem II protein
Photosystem II reaction center protein Psb30 Chains: V, v
Molecule details ›
Chains: V, v
Length: 32 amino acids
Theoretical weight: 3.22 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: D0FY13 (Residues: 2-33; Coverage: 97%)
Gene names: psb30, ycf12
Sequence domains: Photosystem II complex subunit Ycf12
Photosystem II CP43 reaction center protein Chains: C, c
Molecule details ›
Chains: C, c
Length: 449 amino acids
Theoretical weight: 49.13 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: D0FXY3 (Residues: 13-461; Coverage: 97%)
Gene name: psbC
Sequence domains: Photosystem II protein
Photosystem II D2 protein Chains: D, d
Molecule details ›
Chains: D, d
Length: 348 amino acids
Theoretical weight: 38.97 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: A0A1C8XRK9 (Residues: 5-352; Coverage: 99%)
Gene name: psbD
Sequence domains: Photosynthetic reaction centre protein
Cytochrome b559 subunit alpha Chains: E, e
Molecule details ›
Chains: E, e
Length: 76 amino acids
Theoretical weight: 8.74 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: D0FY01 (Residues: 7-82; Coverage: 93%)
Gene name: psbE
Sequence domains:
Cytochrome b559 subunit beta Chains: F, f
Molecule details ›
Chains: F, f
Length: 31 amino acids
Theoretical weight: 3.55 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: A0A1C8XRP4 (Residues: 14-44; Coverage: 71%)
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: 67 amino acids
Theoretical weight: 7.12 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: A0A1C8XRP3 (Residues: 15-81; Coverage: 81%)
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: 3.93 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: D0FXX5 (Residues: 1-35; Coverage: 95%)
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: 36 amino acids
Theoretical weight: 3.74 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: A0A1C8XRM8 (Residues: 7-42; Coverage: 86%)
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: 4.16 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: D0FXX2 (Residues: 10-46; Coverage: 80%)
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: 4.42 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: D0FY19 (Residues: 1-38; Coverage: 100%)
Gene name: psbL
Sequence domains: PsbL protein
Photosystem II reaction center protein M Chains: M, m
Molecule details ›
Chains: M, m
Length: 31 amino acids
Theoretical weight: 3.31 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: D0FXZ3 (Residues: 3-33; Coverage: 84%)
Gene name: psbM
Sequence domains: Photosystem II reaction centre M protein (PsbM)
PsbO Chains: O, o
Molecule details ›
Chains: O, o
Length: 238 amino acids
Theoretical weight: 25.9 KDa
Source organism: Dunaliella salina
PsbP Chains: P, p
Molecule details ›
Chains: P, p
Length: 187 amino acids
Theoretical weight: 20.43 KDa
Source organism: Dunaliella salina
Photosystem II reaction center protein T Chains: T, t
Molecule details ›
Chains: T, t
Length: 30 amino acids
Theoretical weight: 3.48 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: D0FY04 (Residues: 1-30; Coverage: 97%)
Gene name: psbT
Sequence domains: Photosystem II reaction centre T protein
PsbW Chains: W, w
Molecule details ›
Chains: W, w
Length: 44 amino acids
Theoretical weight: 4.7 KDa
Source organism: Dunaliella salina
PsbX Chains: X, x
Molecule details ›
Chains: X, x
Length: 30 amino acids
Theoretical weight: 2.85 KDa
Source organism: Dunaliella salina
Photosystem II reaction center protein Z Chains: Z, z
Molecule details ›
Chains: Z, z
Length: 61 amino acids
Theoretical weight: 6.43 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: D0FXZ2 (Residues: 1-61; Coverage: 97%)
Gene name: psbZ
Sequence domains: YCF9
Chlorophyll a-b binding protein of LHCII type I, chloroplastic Chain: N
Molecule details ›
Chain: N
Length: 222 amino acids
Theoretical weight: 24.08 KDa
Source organism: Dunaliella salina
Chlorophyll a-b binding protein, chloroplastic Chain: G
Molecule details ›
Chain: G
Length: 221 amino acids
Theoretical weight: 23.72 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: A1XKU7 (Residues: 32-252; Coverage: 87%)
Sequence domains: Chlorophyll A-B binding protein
CP26 Chain: S
Molecule details ›
Chain: S
Length: 243 amino acids
Theoretical weight: 26.23 KDa
Source organism: Dunaliella salina
LHCII M1 Chain: Y
Molecule details ›
Chain: Y
Length: 222 amino acids
Theoretical weight: 23.57 KDa
Source organism: Dunaliella salina
PsbU Chains: U, u
Molecule details ›
Chains: U, u
Length: 27 amino acids
Theoretical weight: 3.22 KDa
Source organism: Dunaliella salina

Ligands and Environments


Cofactor: Ligand HEM 2 x HEM
26 bound ligands:
Ligand OEX 2 x OEX
Ligand FE2 2 x FE2
Ligand CL 4 x CL
Ligand CLA 106 x CLA
Ligand PHO 4 x PHO
Ligand BCR 16 x BCR
Ligand SQD 10 x SQD
Ligand LMG 14 x LMG
Ligand SPH 3 x SPH
Ligand C7Z 2 x C7Z
Ligand DGD 8 x DGD
Ligand 3PH 5 x 3PH
Ligand DGA 6 x DGA
Ligand LHG 14 x LHG
Ligand LMK 2 x LMK
Ligand BCT 2 x BCT
Ligand PL9 2 x PL9
Ligand RRX 2 x RRX
Ligand GOL 1 x GOL
Ligand 4RF 4 x 4RF
Ligand CHL 21 x CHL
Ligand LUT 8 x LUT
Ligand XAT 3 x XAT
Ligand NEX 4 x NEX
Ligand LPX 1 x LPX
Ligand PTY 2 x PTY
1 modified residue:
Ligand CSD 2 x CSD

Experiments and Validation Details

Entry percentile scores
Resolution: 3.61Å
Relevant EMDB volumes: EMD-13548

Quick links

Citations

3 citation in other articles

Structure of Dunaliella photosystem II reveals conformational flexibility of stacked and unstacked supercomplexes.
Caspy et al. (2023)
2 more