› 7d1u

Electron Microscopy
2.08Å resolution

Cryo-EM Structure of PSII at 2.08 angstrom resolution

Released:
DOI: 10.2210/pdb7d1u/pdb
PDB entry 7d1u coloured by chain, front view.
PDB entry 7d1u coloured by chain, side view.
PDB entry 7d1u coloured by chain, top view.
Source organism: Thermostichus vulcanus
Primary publication:
High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams.
Kato K, Miyazaki N, Hamaguchi T, Nakajima Y, Akita F, Yonekura K, Shen JR
Commun Biol 4 382 (2021)
PMID: 33753866
Related structures: EMD-30548

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 40-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112071 (preferred)
Entry contents:
20 distinct polypeptide molecules
Macromolecules (20 distinct):
Photosystem II protein D1 Chains: A, a
Molecule details ›
Chains: A, 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 Chains: B, b
Molecule details ›
Chains: B, b
Length: 505 amino acids
Theoretical weight: 56.07 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR1 (Residues: 1-505; Coverage: 100%)
Gene name: psbB
Sequence domains: Photosystem II protein
Photosystem II CP43 reaction center protein Chains: C, c
Molecule details ›
Chains: C, 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 Chains: D, d
Molecule details ›
Chains: D, d
Length: 342 amino acids
Theoretical weight: 38.42 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR8 (Residues: 1-342; Coverage: 100%)
Gene name: psbD
Sequence domains: Photosynthetic reaction centre protein
Cytochrome b559 subunit alpha Chains: E, e
Molecule details ›
Chains: E, e
Length: 81 amino acids
Theoretical weight: 9.32 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12238 (Residues: 4-84; Coverage: 96%)
Gene name: psbE
Sequence domains:
Cytochrome b559 subunit beta Chains: F, f
Molecule details ›
Chains: F, f
Length: 34 amino acids
Theoretical weight: 3.87 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12239 (Residues: 12-45; Coverage: 76%)
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: 63 amino acids
Theoretical weight: 7.06 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P19052 (Residues: 1-63; Coverage: 97%)
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: 36 amino acids
Theoretical weight: 4.2 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12240 (Residues: 1-36; 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: 37 amino acids
Theoretical weight: 3.76 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: Q7DGD4 (Residues: 4-40; Coverage: 93%)
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: 4.1 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 Chains: L, l
Molecule details ›
Chains: L, 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 Chains: M, m
Molecule details ›
Chains: M, m
Length: 34 amino acids
Theoretical weight: 3.84 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12312 (Residues: 1-34; Coverage: 94%)
Gene name: psbM
Sequence domains: Photosystem II reaction centre M protein (PsbM)
Photosystem II extrinsic protein O Chains: O, o
Molecule details ›
Chains: O, 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 Chains: T, t
Molecule details ›
Chains: T, t
Length: 31 amino acids
Theoretical weight: 3.78 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12313 (Residues: 1-31; Coverage: 97%)
Gene name: psbT
Sequence domains: Photosystem II reaction centre T protein
Photosystem II extrinsic protein U Chains: U, u
Molecule details ›
Chains: U, u
Length: 97 amino acids
Theoretical weight: 10.97 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P56152 (Residues: 8-104; Coverage: 93%)
Gene name: psbU
Sequence domains: Photosystem II 12 kDa extrinsic protein (PsbU)
Photosystem II extrinsic protein V Chains: V, v
Molecule details ›
Chains: V, v
Length: 137 amino acids
Theoretical weight: 15.15 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P0A387 (Residues: 27-163; Coverage: 100%)
Gene name: psbV
Sequence domains: Cytochrome c-550 domain
Photosystem II reaction center protein Psb30 Chains: Y, y
Molecule details ›
Chains: Y, 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 Chains: X, x
Molecule details ›
Chains: X, 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 Chains: Z, z
Molecule details ›
Chains: Z, 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 Chains: R, r
Molecule details ›
Chains: R, 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 2 x HEC

Cofactor: Ligand HEM 2 x HEM
16 bound ligands:
Ligand OEX 2 x OEX
Ligand FE2 2 x FE2
Ligand CL 4 x CL
Ligand CLA 70 x CLA
Ligand PHO 4 x PHO
Ligand BCR 20 x BCR
Ligand SQD 8 x SQD
Ligand PL9 4 x PL9
Ligand UNL 36 x UNL
Ligand BCT 2 x BCT
Ligand LMG 10 x LMG
Ligand LHG 10 x LHG
Ligand DGD 8 x DGD
Ligand RRX 2 x RRX
Ligand LMT 8 x LMT
Ligand MG 2 x MG
2 modified residues:
Ligand HSK 2 x HSK
Ligand FME 6 x FME

Experiments and Validation Details

Entry percentile scores
Resolution: 2.08Å
Relevant EMDB volumes: EMD-30548

Quick links

Citations

6 review citations

Evolutionary diversity of proton and water channels on the oxidizing side of photosystem II and their relevance to function.
Hussein et al. (2023)
5 more

3 mentions without citation

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