› 3kzi

X-ray diffraction
3.6Å resolution

Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II

Released:
DOI: 10.2210/pdb3kzi/pdb
PDB entry 3kzi coloured by chain, front view.
PDB entry 3kzi coloured by chain, side view.
PDB entry 3kzi coloured by chain, top view.
Source organism: Thermosynechococcus vestitus BP-1
Primary publication:
Crystal structure of monomeric photosystem II from Thermosynechococcus elongatus at 3.6-a resolution.
Broser M, Gabdulkhakov A, Kern J, Guskov A, Müh F, Saenger W, Zouni A
J Biol Chem 285 26255-62 (2010)
PMID: 20558739

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 nonadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141174 (preferred)
Entry contents:
19 distinct polypeptide molecules
Macromolecules (19 distinct):
Photosystem II protein D1 1 Chain: A
Molecule details ›
Chain: A
Length: 344 amino acids
Theoretical weight: 38.27 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: P0A444 (Residues: 1-344; Coverage: 96%)
Gene names: psbA-1, psbA1, tlr1843
Sequence domains: Photosynthetic reaction centre protein
Photosystem II CP47 reaction center protein Chain: B
Molecule details ›
Chain: B
Length: 510 amino acids
Theoretical weight: 56.66 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DIQ1 (Residues: 1-510; Coverage: 100%)
Gene names: psbB, tlr1530
Sequence domains: Photosystem II protein
Structure domains: Photosystem II CP47 reaction center protein
Photosystem II CP43 reaction center protein Chain: C
Molecule details ›
Chain: C
Length: 461 amino acids
Theoretical weight: 50.29 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DIF8 (Residues: 1-461; Coverage: 100%)
Gene names: psbC, tlr1631
Sequence domains: Photosystem II protein
Structure domains: photosystem ii from thermosynechococcus elongatus
Photosystem II D2 protein Chain: D
Molecule details ›
Chain: D
Length: 352 amino acids
Theoretical weight: 39.39 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8CM25 (Residues: 1-352; Coverage: 100%)
Gene names: psbD1, psbD2, tlr0455, tlr1630
Sequence domains: Photosynthetic reaction centre protein
Cytochrome b559 subunit alpha Chain: E
Molecule details ›
Chain: E
Length: 83 amino acids
Theoretical weight: 9.45 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DIP0 (Residues: 2-84; Coverage: 99%)
Gene names: psbE, tsr1541
Sequence domains:
Structure domains: Photosystem II cytochrome b559, alpha subunit
Cytochrome b559 subunit beta Chain: F
Molecule details ›
Chain: F
Length: 44 amino acids
Theoretical weight: 4.94 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DIN9 (Residues: 2-45; Coverage: 98%)
Gene names: psbF, tsr1542
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: 65 amino acids
Theoretical weight: 7.23 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DJ43 (Residues: 2-66; Coverage: 99%)
Gene names: psbH, tsl1386
Sequence domains: Photosystem II 10 kDa phosphoprotein
Structure domains: Photosystem II reaction center protein H
Photosystem II reaction center protein I Chain: I
Molecule details ›
Chain: I
Length: 38 amino acids
Theoretical weight: 4.41 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DJZ6 (Residues: 1-38; Coverage: 100%)
Gene names: psbI, tsr1074
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: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: P59087 (Residues: 1-40; Coverage: 100%)
Gene names: psbJ, tsr1544
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: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q9F1K9 (Residues: 10-46; Coverage: 80%)
Gene names: psbK, tsl0176
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: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DIN8 (Residues: 1-37; Coverage: 100%)
Gene names: psbL, tsr1543
Sequence domains: PsbL protein
Photosystem II reaction center protein M Chain: M
Molecule details ›
Chain: M
Length: 36 amino acids
Theoretical weight: 3.98 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DHA7 (Residues: 1-36; Coverage: 100%)
Gene names: psbM, tsl2052
Sequence domains: Photosystem II reaction centre M protein (PsbM)
Photosystem II extrinsic protein O Chain: O
Molecule details ›
Chain: O
Length: 246 amino acids
Theoretical weight: 26.85 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: P0A431 (Residues: 27-272; Coverage: 100%)
Gene names: psbO, tll0444
Sequence domains: Manganese-stabilising protein / photosystem II polypeptide
Structure domains:
Photosystem II reaction center protein T Chain: T
Molecule details ›
Chain: T
Length: 32 amino acids
Theoretical weight: 3.88 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DIQ0 (Residues: 1-32; Coverage: 100%)
Gene names: psbT, tsr1531
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: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q9F1L5 (Residues: 31-134; Coverage: 100%)
Gene names: psbU, tll2409
Sequence domains: Photosystem II 12 kDa extrinsic protein (PsbU)
Structure domains: Photosystem II 12 kDa extrinsic protein
Photosystem II extrinsic protein V Chain: V
Molecule details ›
Chain: V
Length: 137 amino acids
Theoretical weight: 15.15 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: P0A386 (Residues: 27-163; Coverage: 100%)
Gene names: psbV, tll1285
Sequence domains: Cytochrome c-550 domain
Structure domains: Cytochrome c-like domain
Photosystem II reaction center protein Psb30 Chain: y
Molecule details ›
Chain: y
Length: 46 amino acids
Theoretical weight: 5.04 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DJI1 (Residues: 1-46; Coverage: 100%)
Gene names: psb30, tsr1242, 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: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q9F1R6 (Residues: 2-41; Coverage: 98%)
Gene names: psbX, tsr2013
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: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DHJ2 (Residues: 1-62; Coverage: 100%)
Gene names: psbZ, tsr1967
Sequence domains: YCF9
Structure domains: Photosystem II PsbZ, reaction centre

Ligands and Environments


Cofactor: Ligand HEM 2 x HEM
14 bound ligands:
Ligand FE2 1 x FE2
Ligand CLA 35 x CLA
Ligand PHO 2 x PHO
Ligand MES 1 x MES
Ligand OEC 1 x OEC
Ligand BCR 11 x BCR
Ligand LHG 2 x LHG
Ligand LMG 8 x LMG
Ligand DGD 8 x DGD
Ligand LMT 7 x LMT
Ligand SQD 4 x SQD
Ligand BCT 1 x BCT
Ligand PL9 1 x PL9
Ligand CA 3 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: C2221
Unit cell:
a: 119.89Å b: 224.69Å c: 337.28Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.297 0.297 0.308

Quick links

Citations

9 review citations

Mn4Ca cluster in photosynthesis: where and how water is oxidized to dioxygen.
Yano et al. (2014)
8 more

5 mentions without citation

Structural insights into photosystem II assembly.
Zabret et al. (2021)
4 more