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

Electron Microscopy
2.58Å resolution
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
Assembly composition:
hetero tridecamer (preferred)
Entry contents: 13 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Photosystem II
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Multimeric state: hetero tridecamer
PDBe Complex ID: PDB-CPX-138665

Macromolecules

Photosystem II protein D1 2
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
Pfam: Photosynthetic reaction centre protein
InterPro:
Photosystem II protein D1 2 in PDB entry 6wj6, assembly 1, front view.
Photosystem II protein D1 2 in PDB entry 6wj6, assembly 1, side view.
Photosystem II protein D1 2 in PDB entry 6wj6, assembly 1, top view.
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Photosystem II CP47 reaction center protein
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
Pfam: Photosystem II protein
InterPro:
Photosystem II CP47 reaction center protein in PDB entry 6wj6, assembly 1, front view.
Photosystem II CP47 reaction center protein in PDB entry 6wj6, assembly 1, side view.
Photosystem II CP47 reaction center protein in PDB entry 6wj6, assembly 1, top view.
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Photosystem II CP43 reaction center protein
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
Pfam: Photosystem II protein
InterPro:
Photosystem II CP43 reaction center protein in PDB entry 6wj6, assembly 1, front view.
Photosystem II CP43 reaction center protein in PDB entry 6wj6, assembly 1, side view.
Photosystem II CP43 reaction center protein in PDB entry 6wj6, assembly 1, top view.
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Photosystem II D2 protein
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
Pfam: Photosynthetic reaction centre protein
InterPro:
Photosystem II D2 protein in PDB entry 6wj6, assembly 1, front view.
Photosystem II D2 protein in PDB entry 6wj6, assembly 1, side view.
Photosystem II D2 protein in PDB entry 6wj6, assembly 1, top view.
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Cytochrome b559 subunit alpha
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
Pfam:
InterPro:
Cytochrome b559 subunit alpha in PDB entry 6wj6, assembly 1, front view.
Cytochrome b559 subunit alpha in PDB entry 6wj6, assembly 1, side view.
Cytochrome b559 subunit alpha in PDB entry 6wj6, assembly 1, top view.
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Cytochrome b559 subunit beta
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
Pfam: Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits
InterPro:
Cytochrome b559 subunit beta in PDB entry 6wj6, assembly 1, front view.
Cytochrome b559 subunit beta in PDB entry 6wj6, assembly 1, side view.
Cytochrome b559 subunit beta in PDB entry 6wj6, assembly 1, top view.
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Photosystem II reaction center protein H
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
Pfam: Photosystem II 10 kDa phosphoprotein
InterPro:
Photosystem II reaction center protein H in PDB entry 6wj6, assembly 1, front view.
Photosystem II reaction center protein H in PDB entry 6wj6, assembly 1, side view.
Photosystem II reaction center protein H in PDB entry 6wj6, assembly 1, top view.
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Photosystem II reaction center protein I
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
Pfam: Photosystem II reaction centre I protein (PSII 4.8 kDa protein)
InterPro:
Photosystem II reaction center protein I in PDB entry 6wj6, assembly 1, front view.
Photosystem II reaction center protein I in PDB entry 6wj6, assembly 1, side view.
Photosystem II reaction center protein I in PDB entry 6wj6, assembly 1, top view.
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Photosystem II reaction center protein K
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
Pfam: Photosystem II 4 kDa reaction centre component
InterPro:
Photosystem II reaction center protein K in PDB entry 6wj6, assembly 1, front view.
Photosystem II reaction center protein K in PDB entry 6wj6, assembly 1, side view.
Photosystem II reaction center protein K in PDB entry 6wj6, assembly 1, top view.
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Photosystem II reaction center protein L
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
Pfam: PsbL protein
InterPro:
Photosystem II reaction center protein L in PDB entry 6wj6, assembly 1, front view.
Photosystem II reaction center protein L in PDB entry 6wj6, assembly 1, side view.
Photosystem II reaction center protein L in PDB entry 6wj6, assembly 1, top view.
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Photosystem II reaction center protein M
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
Pfam: Photosystem II reaction centre M protein (PsbM)
InterPro:
Photosystem II reaction center protein M in PDB entry 6wj6, assembly 1, front view.
Photosystem II reaction center protein M in PDB entry 6wj6, assembly 1, side view.
Photosystem II reaction center protein M in PDB entry 6wj6, assembly 1, top view.
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Photosystem II reaction center protein T
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
Pfam: Photosystem II reaction centre T protein
InterPro:
Photosystem II reaction center protein T in PDB entry 6wj6, assembly 1, front view.
Photosystem II reaction center protein T in PDB entry 6wj6, assembly 1, side view.
Photosystem II reaction center protein T in PDB entry 6wj6, assembly 1, top view.
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Photosystem II reaction center protein X
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
Pfam: Photosystem II reaction centre X protein (PsbX)
InterPro:
Photosystem II reaction center protein X in PDB entry 6wj6, assembly 1, front view.
Photosystem II reaction center protein X in PDB entry 6wj6, assembly 1, side view.
Photosystem II reaction center protein X in PDB entry 6wj6, assembly 1, top view.
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