› 6wj6

Electron Microscopy
2.58Å resolution

Cryo-EM structure of apo-Photosystem II from Synechocystis sp. PCC 6803

Released:
DOI: 10.2210/pdb6wj6/pdb
PDB entry 6wj6 coloured by chain, front view.
PDB entry 6wj6 coloured by chain, side view.
PDB entry 6wj6 coloured by chain, top view.
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
Primary publication:
Cryo-EM Structure of Monomeric Photosystem II from Synechocystis sp. PCC 6803 Lacking the Water-Oxidation Complex
Gisriel CJ, Zhou K, Huang H, Debus RJ, Xiong Y, Brudvig GW
Joule (2020)
Related structures: EMD-21690

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 tridecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138665 (preferred)
Entry contents:
13 distinct polypeptide molecules
Macromolecules (13 distinct):
Photosystem II protein D1 2 Chain: A
Molecule details ›
Chain: A
Length: 360 amino acids
Theoretical weight: 39.74 KDa
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
UniProt:
  • Canonical: P16033 (Residues: 1-360; Coverage: 100%)
Gene names: psbA-2, psbA-3, psbA2, psbA3, sll1867, slr1311
Sequence domains: Photosynthetic reaction centre protein
Photosystem II CP47 reaction center protein Chain: B
Molecule details ›
Chain: B
Length: 507 amino acids
Theoretical weight: 55.95 KDa
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
UniProt:
  • Canonical: P05429 (Residues: 1-507; Coverage: 100%)
Gene names: psbB, slr0906
Sequence domains: Photosystem II protein
Photosystem II CP43 reaction center protein Chain: C
Molecule details ›
Chain: C
Length: 460 amino acids
Theoretical weight: 50.33 KDa
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
UniProt:
  • Canonical: P09193 (Residues: 1-460; Coverage: 100%)
Gene names: psbC, sll0851
Sequence domains: Photosystem II protein
Photosystem II D2 protein Chain: D
Molecule details ›
Chain: D
Length: 352 amino acids
Theoretical weight: 39.52 KDa
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
UniProt:
  • Canonical: P09192 (Residues: 1-352; Coverage: 100%)
Gene names: psbD, sll0849
Sequence domains: Photosynthetic reaction centre protein
Cytochrome b559 subunit alpha Chain: E
Molecule details ›
Chain: E
Length: 81 amino acids
Theoretical weight: 9.45 KDa
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
UniProt:
  • Canonical: P09190 (Residues: 1-81; Coverage: 100%)
Gene names: psbE, ssr3451
Sequence domains:
Cytochrome b559 subunit beta Chain: F
Molecule details ›
Chain: F
Length: 44 amino acids
Theoretical weight: 4.94 KDa
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
UniProt:
  • Canonical: P09191 (Residues: 1-44; Coverage: 100%)
Gene names: psbF, smr0006
Sequence domains: Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits
Photosystem II reaction center protein H Chain: H
Molecule details ›
Chain: H
Length: 64 amino acids
Theoretical weight: 7.12 KDa
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
UniProt:
  • Canonical: P14835 (Residues: 1-64; Coverage: 100%)
Gene names: psbH, ssl2598
Sequence domains: Photosystem II 10 kDa phosphoprotein
Photosystem II reaction center protein I Chain: I
Molecule details ›
Chain: I
Length: 38 amino acids
Theoretical weight: 4.31 KDa
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
UniProt:
  • Canonical: Q54697 (Residues: 1-38; Coverage: 100%)
Gene names: psbI, sml0001
Sequence domains: Photosystem II reaction centre I protein (PSII 4.8 kDa protein)
Photosystem II reaction center protein K Chain: K
Molecule details ›
Chain: K
Length: 45 amino acids
Theoretical weight: 5.11 KDa
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
UniProt:
  • Canonical: P15819 (Residues: 1-45; Coverage: 100%)
Gene names: psbK, sml0005
Sequence domains: Photosystem II 4 kDa reaction centre component
Photosystem II reaction center protein L Chain: L
Molecule details ›
Chain: L
Length: 39 amino acids
Theoretical weight: 4.48 KDa
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
UniProt:
  • Canonical: Q55354 (Residues: 1-39; Coverage: 100%)
Gene names: psbL, smr0007
Sequence domains: PsbL protein
Photosystem II reaction center protein M Chain: M
Molecule details ›
Chain: M
Length: 35 amino acids
Theoretical weight: 3.88 KDa
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
UniProt:
  • Canonical: P72701 (Residues: 1-35; Coverage: 100%)
Gene names: psbM, sml0003
Sequence domains: Photosystem II reaction centre M protein (PsbM)
Photosystem II reaction center protein T Chain: T
Molecule details ›
Chain: T
Length: 31 amino acids
Theoretical weight: 3.54 KDa
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
UniProt:
  • Canonical: P74787 (Residues: 1-31; Coverage: 100%)
Gene names: psbT, smr0001
Sequence domains: Photosystem II reaction centre T protein
Photosystem II reaction center protein X Chain: X
Molecule details ›
Chain: X
Length: 39 amino acids
Theoretical weight: 4.19 KDa
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
UniProt:
  • Canonical: P72575 (Residues: 1-39; Coverage: 100%)
Gene names: psbX, sml0002
Sequence domains: Photosystem II reaction centre X protein (PsbX)

Ligands and Environments


Cofactor: Ligand HEM 1 x HEM
13 bound ligands:
Ligand FE2 1 x FE2
Ligand CLA 35 x CLA
Ligand PHO 2 x PHO
Ligand BCR 9 x BCR
Ligand SQD 7 x SQD
Ligand PL9 2 x PL9
Ligand LMG 3 x LMG
Ligand LMT 2 x LMT
Ligand DGD 2 x DGD
Ligand CL 1 x CL
Ligand BCT 1 x BCT
Ligand LHG 4 x LHG
Ligand FME 3 x FME
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.58Å
Relevant EMDB volumes: EMD-21690

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