› 7piw

Electron Microscopy
4Å resolution

Stacked stretched Dunaliella PSII

Released:
DOI: 10.2210/pdb7piw/pdb
PDB entry 7piw coloured by chain, front view.
PDB entry 7piw coloured by chain, side view.
PDB entry 7piw 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-13455

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 99-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111979 (preferred)
Entry contents:
27 distinct polypeptide molecules
Macromolecules (27 distinct):
Photosystem II protein D1 Chains: A, A1, a, a1
Molecule details ›
Chains: A, A1, a, a1
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, B1, b, b1
Molecule details ›
Chains: B, B1, b, b1
Length: 484 amino acids
Theoretical weight: 53.29 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: D0FY05 (Residues: 2-485; Coverage: 95%)
Gene name: psbB
Sequence domains: Photosystem II protein
Photosystem II reaction center protein Psb30 Chains: V, V1, v, v1
Molecule details ›
Chains: V, V1, v, v1
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, C1, c, c1
Molecule details ›
Chains: C, C1, c, c1
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, D1, d, d1
Molecule details ›
Chains: D, D1, d, d1
Length: 348 amino acids
Theoretical weight: 38.97 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: D0FXW8 (Residues: 5-352; Coverage: 99%)
Gene name: psbD
Sequence domains: Photosynthetic reaction centre protein
Cytochrome b559 subunit alpha Chains: E, E1, e, e1
Molecule details ›
Chains: E, E1, e, e1
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, F1, f, f1
Molecule details ›
Chains: F, F1, f, f1
Length: 31 amino acids
Theoretical weight: 3.55 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: D0FY18 (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, H1, h, h1
Molecule details ›
Chains: H, H1, h, h1
Length: 67 amino acids
Theoretical weight: 7.12 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: D0FY02 (Residues: 15-81; Coverage: 81%)
Gene name: psbH
Sequence domains: Photosystem II 10 kDa phosphoprotein
Photosystem II reaction center protein I Chains: I, I1, i, i1
Molecule details ›
Chains: I, I1, i, i1
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, J1, j, j1
Molecule details ›
Chains: J, J1, j, j1
Length: 36 amino acids
Theoretical weight: 3.74 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: D0FXW2 (Residues: 8-41; Coverage: 81%)
Gene name: psbJ
Sequence domains: PsbJ
Photosystem II reaction center protein K Chains: K, K1, k, k1
Molecule details ›
Chains: K, K1, k, k1
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, L1, l
Molecule details ›
Chains: L, L1, 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: 32 amino acids
Theoretical weight: 3.44 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: D0FXZ3 (Residues: 2-33; Coverage: 87%)
Gene name: psbM
Sequence domains: Photosystem II reaction centre M protein (PsbM)
PsbO Chains: O, O1, o, o1
Molecule details ›
Chains: O, O1, o, o1
Length: 238 amino acids
Theoretical weight: 25.87 KDa
Source organism: Dunaliella salina
PsbP Chains: P, P1, p, p1
Molecule details ›
Chains: P, P1, p, p1
Length: 187 amino acids
Theoretical weight: 20.43 KDa
Source organism: Dunaliella salina
Photosystem II reaction center protein T Chains: T, T1, t, t1
Molecule details ›
Chains: T, T1, t, t1
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, W1, w, w1
Molecule details ›
Chains: W, W1, w, w1
Length: 44 amino acids
Theoretical weight: 4.7 KDa
Source organism: Dunaliella salina
PsbX Chains: X, X1, x, x1
Molecule details ›
Chains: X, X1, x, x1
Length: 30 amino acids
Theoretical weight: 2.85 KDa
Source organism: Dunaliella salina
PsbZ Chains: Z, Z1, z, z1
Molecule details ›
Chains: Z, Z1, z, z1
Length: 61 amino acids
Theoretical weight: 6.43 KDa
Source organism: Dunaliella salina
LHCII M3 Chains: N, N1, n, n1
Molecule details ›
Chains: N, N1, n, n1
Length: 222 amino acids
Theoretical weight: 24.08 KDa
Source organism: Dunaliella salina
LHCII M2 Chains: G, G1, g, g1
Molecule details ›
Chains: G, G1, g, g1
Length: 221 amino acids
Theoretical weight: 23.72 KDa
Source organism: Dunaliella salina
CP29 Chains: R, r
Molecule details ›
Chains: R, r
Length: 202 amino acids
Theoretical weight: 21.75 KDa
Source organism: Dunaliella salina
CP26 Chains: S, S1, s, s1
Molecule details ›
Chains: S, S1, s, s1
Length: 243 amino acids
Theoretical weight: 26.23 KDa
Source organism: Dunaliella salina
LHCII M1 Chains: Y, Y1, y, y1
Molecule details ›
Chains: Y, Y1, y, y1
Length: 222 amino acids
Theoretical weight: 23.54 KDa
Source organism: Dunaliella salina
PsbU Chains: U, U1, u, u1
Molecule details ›
Chains: U, U1, u, u1
Length: 27 amino acids
Theoretical weight: 3.22 KDa
Source organism: Dunaliella salina
Photosystem II reaction center protein M Chains: M1, m1
Molecule details ›
Chains: M1, m1
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)
CP29 Chains: R1, r1
Molecule details ›
Chains: R1, r1
Length: 202 amino acids
Theoretical weight: 21.83 KDa
Source organism: Dunaliella salina

Ligands and Environments


Cofactor: Ligand HEM 4 x HEM
29 bound ligands:
Ligand OEX 4 x OEX
Ligand FE2 4 x FE2
Ligand CL 8 x CL
Ligand CLA 316 x CLA
Ligand PHO 8 x PHO
Ligand BCR 32 x BCR
Ligand SQD 16 x SQD
Ligand LMG 26 x LMG
Ligand NA 4 x NA
Ligand C7Z 4 x C7Z
Ligand DGA 10 x DGA
Ligand GOL 5 x GOL
Ligand DGD 16 x DGD
Ligand LHG 35 x LHG
Ligand LMK 4 x LMK
Ligand BCT 4 x BCT
Ligand PL9 4 x PL9
Ligand RRX 4 x RRX
Ligand CHL 92 x CHL
Ligand LUT 36 x LUT
Ligand XAT 16 x XAT
Ligand NEX 20 x NEX
Ligand LPX 4 x LPX
Ligand 3PH 9 x 3PH
Ligand SPH 6 x SPH
Ligand 4RF 4 x 4RF
Ligand LMT 2 x LMT
Ligand ERG 2 x ERG
Ligand PTY 4 x PTY
1 modified residue:
Ligand SEP 2 x SEP

Experiments and Validation Details

Entry percentile scores
Resolution: 4Å
Relevant EMDB volumes: EMD-13455

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