› 7eda

Electron Microscopy
2.78Å resolution

Structure of monomeric photosystem II

Released:
DOI: 10.2210/pdb7eda/pdb
PDB entry 7eda coloured by chain, front view.
PDB entry 7eda coloured by chain, side view.
PDB entry 7eda coloured by chain, top view.
Source organism: Thermostichus vulcanus
Primary publication:
Cryo-EM structure of monomeric photosystem II at 2.78 Å resolution reveals factors important for the formation of dimer.
Yu H, Hamaguchi T, Nakajima Y, Kato K, Kawakami K, Akita F, Yonekura K, Shen JR
Biochim Biophys Acta Bioenerg 1862 148471 (2021)
PMID: 34216574
Related structures: EMD-31062

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 icosamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112066 (preferred)
Entry contents:
20 distinct polypeptide molecules
Macromolecules (20 distinct):
Photosystem II protein D1 Chain: A
Molecule details ›
Chain: A
Length: 334 amino acids
Theoretical weight: 37.03 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P51765 (Residues: 11-344; Coverage: 93%)
Gene names: psbA, psbA-1
Sequence domains: Photosynthetic reaction centre protein
Photosystem II CP47 reaction center protein Chain: B
Molecule details ›
Chain: B
Length: 504 amino acids
Theoretical weight: 55.94 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR1 (Residues: 1-504; Coverage: 100%)
Gene name: psbB
Sequence domains: Photosystem II protein
Photosystem II CP43 reaction center protein Chain: C
Molecule details ›
Chain: C
Length: 451 amino acids
Theoretical weight: 49.21 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR7 (Residues: 1-451; Coverage: 100%)
Gene name: psbC
Sequence domains: Photosystem II protein
Photosystem II D2 protein Chain: D
Molecule details ›
Chain: D
Length: 341 amino acids
Theoretical weight: 38.29 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR8 (Residues: 2-342; Coverage: 100%)
Gene name: psbD
Sequence domains: Photosynthetic reaction centre protein
Cytochrome b559 subunit alpha Chain: E
Molecule details ›
Chain: E
Length: 84 amino acids
Theoretical weight: 9.58 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12238 (Residues: 1-84; Coverage: 100%)
Gene name: psbE
Sequence domains:
Cytochrome b559 subunit beta Chain: F
Molecule details ›
Chain: F
Length: 45 amino acids
Theoretical weight: 5.07 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12239 (Residues: 1-45; Coverage: 100%)
Gene name: psbF
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: 62 amino acids
Theoretical weight: 6.99 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P19052 (Residues: 1-62; Coverage: 95%)
Gene name: psbH
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: 4.44 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12240 (Residues: 1-38; Coverage: 100%)
Gene name: psbI
Sequence domains: Photosystem II reaction centre I protein (PSII 4.8 kDa protein)
Photosystem II reaction center protein J Chain: J
Molecule details ›
Chain: J
Length: 40 amino acids
Theoretical weight: 4.11 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: Q7DGD4 (Residues: 1-40; Coverage: 100%)
Gene name: psbJ
Sequence domains: PsbJ
Photosystem II reaction center protein K Chain: K
Molecule details ›
Chain: K
Length: 37 amino acids
Theoretical weight: 4.1 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P19054 (Residues: 1-37; Coverage: 100%)
Gene name: psbK
Sequence domains: Photosystem II 4 kDa reaction centre component
Photosystem II reaction center protein L Chain: L
Molecule details ›
Chain: L
Length: 37 amino acids
Theoretical weight: 4.3 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12241 (Residues: 1-37; Coverage: 100%)
Gene name: psbL
Sequence domains: PsbL protein
Photosystem II reaction center protein M Chain: M
Molecule details ›
Chain: M
Length: 30 amino acids
Theoretical weight: 3.29 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12312 (Residues: 3-32; Coverage: 83%)
Gene name: psbM
Sequence domains: Photosystem II reaction centre M protein (PsbM)
Photosystem II extrinsic protein O Chain: O
Molecule details ›
Chain: O
Length: 244 amino acids
Theoretical weight: 26.65 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR2 (Residues: 1-244; Coverage: 100%)
Gene name: psbO
Sequence domains: Manganese-stabilising protein / photosystem II polypeptide
Photosystem II reaction center protein T Chain: T
Molecule details ›
Chain: T
Length: 30 amino acids
Theoretical weight: 3.65 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12313 (Residues: 1-30; Coverage: 94%)
Gene name: psbT
Sequence domains: Photosystem II reaction centre T protein
Photosystem II extrinsic protein U Chain: U
Molecule details ›
Chain: U
Length: 104 amino acids
Theoretical weight: 11.66 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P56152 (Residues: 1-104; Coverage: 100%)
Gene name: psbU
Sequence domains: Photosystem II 12 kDa extrinsic protein (PsbU)
Photosystem II extrinsic protein V Chain: V
Molecule details ›
Chain: V
Length: 163 amino acids
Theoretical weight: 18.05 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P0A387 (Residues: 1-163; Coverage: 100%)
Gene name: psbV
Sequence domains: Cytochrome c-550 domain
Photosystem II reaction center protein Psb30 Chain: Y
Molecule details ›
Chain: Y
Length: 30 amino acids
Theoretical weight: 3.23 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR3 (Residues: 1-30; Coverage: 100%)
Gene names: psb30, psbY, ycf12
Sequence domains: Photosystem II complex subunit Ycf12
Photosystem II reaction center protein X Chain: X
Molecule details ›
Chain: X
Length: 40 amino acids
Theoretical weight: 4.19 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR4 (Residues: 1-40; Coverage: 100%)
Gene name: psbX
Sequence domains: Photosystem II reaction centre X protein (PsbX)
Photosystem II reaction center protein Z Chain: Z
Molecule details ›
Chain: Z
Length: 62 amino acids
Theoretical weight: 6.77 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR5 (Residues: 1-62; Coverage: 100%)
Gene name: psbZ
Sequence domains: YCF9
Photosystem II reaction center protein Y Chain: R
Molecule details ›
Chain: R
Length: 34 amino acids
Theoretical weight: 3.86 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P0DM37 (Residues: 1-34; Coverage: 100%)
Gene name: psbY
Sequence domains: Photosystem II protein Y (PsbY)

Ligands and Environments


Cofactor: Ligand HEC 1 x HEC

Cofactor: Ligand HEM 1 x HEM
13 bound ligands:
Ligand OEX 1 x OEX
Ligand FE2 1 x FE2
Ligand CLA 35 x CLA
Ligand PHO 2 x PHO
Ligand BCR 8 x BCR
Ligand SQD 2 x SQD
Ligand LMG 3 x LMG
Ligand PL9 2 x PL9
Ligand UNL 1 x UNL
Ligand DGD 4 x DGD
Ligand BCT 1 x BCT
Ligand LHG 4 x LHG
Ligand RRX 1 x RRX
2 modified residues:
Ligand HSK 1 x HSK
Ligand FME 2 x FME

Experiments and Validation Details

Entry percentile scores
Resolution: 2.78Å
Relevant EMDB volumes: EMD-31062

Quick links

Citations

2 review citations

New Structural and Mechanistic Insights Into Functional Roles of Cytochrome b 559 in Photosystem II.
Chiu et al. (2022)
1 more

2 mentions without citation

An automated pipeline integrating AlphaFold 2 and MODELLER for protein structure prediction.
Gil Zuluaga et al. (2023)
1 more