› 7pi5

Electron Microscopy
2.78Å resolution

Unstacked stretched Dunaliella PSII

Released:
DOI: 10.2210/pdb7pi5/pdb
PDB entry 7pi5 coloured by chain, front view.
PDB entry 7pi5 coloured by chain, side view.
PDB entry 7pi5 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-13430

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 50-mer (preferred)
PDBe Complex ID:
PDB-CPX-103334 (preferred)
Entry contents:
25 distinct polypeptide molecules
Macromolecules (25 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: 53.29 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, 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: 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, o
Molecule details ›
Chains: O, o
Length: 238 amino acids
Theoretical weight: 25.87 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
PSII 6.1 kDa protein Chains: W, w
Molecule details ›
Chains: W, w
Length: 44 amino acids
Theoretical weight: 4.7 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: A0A7S3QU88 (Residues: 65-108; Coverage: 36%)
Gene name: DTER00134_LOCUS7590
Sequence domains: Photosystem II reaction centre W protein (PsbW)
Photosystem II PsbX Chains: X, x
Molecule details ›
Chains: X, x
Length: 30 amino acids
Theoretical weight: 2.85 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: A0A7S3VKF3 (Residues: 103-132; Coverage: 21%)
Gene name: DTER00134_LOCUS5623
Sequence domains: Photosystem II reaction centre X protein (PsbX)
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
LHCII M3 Chains: N, n
Molecule details ›
Chains: N, n
Length: 222 amino acids
Theoretical weight: 24.08 KDa
Source organism: Dunaliella salina
Chlorophyll a-b binding protein, chloroplastic Chains: G, g
Molecule details ›
Chains: G, 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
CP29 Chains: R, r
Molecule details ›
Chains: R, r
Length: 202 amino acids
Theoretical weight: 21.75 KDa
Source organism: Dunaliella salina
Chlorophyll a-b binding protein, chloroplastic Chains: S, s
Molecule details ›
Chains: S, s
Length: 243 amino acids
Theoretical weight: 26.23 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: A0A7S3VRZ8 (Residues: 43-285; Coverage: 85%)
Gene name: DTER00134_LOCUS17631
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chains: Y, y
Molecule details ›
Chains: Y, y
Length: 222 amino acids
Theoretical weight: 23.54 KDa
Source organism: Dunaliella salina
UniProt:
  • Canonical: A0A6S8N9J6 (Residues: 51-272; Coverage: 82%)
Gene names: DTER00134_LOCUS17609, DTER00134_LOCUS17614
Sequence domains: Chlorophyll A-B binding protein
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
25 bound ligands:
Ligand OEX 2 x OEX
Ligand FE2 2 x FE2
Ligand CL 4 x CL
Ligand CLA 160 x CLA
Ligand PHO 4 x PHO
Ligand BCR 16 x BCR
Ligand SQD 6 x SQD
Ligand LMG 12 x LMG
Ligand NA 2 x NA
Ligand C7Z 2 x C7Z
Ligand DGA 4 x DGA
Ligand GOL 4 x GOL
Ligand DGD 8 x DGD
Ligand LHG 18 x LHG
Ligand LMK 2 x LMK
Ligand BCT 2 x BCT
Ligand PL9 2 x PL9
Ligand RRX 2 x RRX
Ligand CHL 46 x CHL
Ligand LUT 18 x LUT
Ligand XAT 8 x XAT
Ligand NEX 10 x NEX
Ligand LPX 2 x LPX
Ligand 3PH 3 x 3PH
Ligand SPH 2 x SPH
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.78Å
Relevant EMDB volumes: EMD-13430

Quick links

Citations

5 citation in other articles

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