› 4fby

X-ray diffraction
6.56Å resolution

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-141178 (preferred)
Entry contents:
20 distinct polypeptide molecules
Macromolecules (20 distinct):
Photosystem II protein D1 1 Chains: A, G
Molecule details ›
Chains: A, G
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 Chains: B, N
Molecule details ›
Chains: B, N
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
Photosystem II CP43 reaction center protein Chains: C, P
Molecule details ›
Chains: C, P
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
Photosystem II D2 protein Chains: D, Q
Molecule details ›
Chains: D, Q
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 Chains: E, R
Molecule details ›
Chains: E, R
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:
Cytochrome b559 subunit beta Chains: F, S
Molecule details ›
Chains: F, S
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 Chains: H, W
Molecule details ›
Chains: H, W
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
Photosystem II reaction center protein I Chains: I, a
Molecule details ›
Chains: I, a
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 Chains: J, b
Molecule details ›
Chains: J, b
Length: 39 amino acids
Theoretical weight: 3.97 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: P59087 (Residues: 2-40; Coverage: 98%)
Gene names: psbJ, tsr1544
Sequence domains: PsbJ
Photosystem II reaction center protein K Chains: K, c
Molecule details ›
Chains: K, c
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 Chains: L, d
Molecule details ›
Chains: L, d
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 Chains: M, e
Molecule details ›
Chains: M, e
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 Chains: O, f
Molecule details ›
Chains: O, f
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
Photosystem II reaction center protein T Chains: T, g
Molecule details ›
Chains: T, g
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 Chains: U, h
Molecule details ›
Chains: U, h
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)
Photosystem II extrinsic protein V Chains: V, i
Molecule details ›
Chains: V, i
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
Photosystem II reaction center protein Psb30 Chains: m, y
Molecule details ›
Chains: m, 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 Chains: X, j
Molecule details ›
Chains: X, j
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 Y Chains: Y, k
Molecule details ›
Chains: Y, k
Length: 28 amino acids
Theoretical weight: 2.4 KDa
Source organism: Thermosynechococcus vestitus BP-1
Photosystem II reaction center protein Z Chains: Z, l
Molecule details ›
Chains: Z, l
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

Ligands and Environments


Cofactor: Ligand HEM 4 x HEM
14 bound ligands:
Ligand CLA 70 x CLA
Ligand PHO 4 x PHO
Ligand PL9 6 x PL9
Ligand DGD 14 x DGD
Ligand LHG 4 x LHG
Ligand SQD 10 x SQD
Ligand LMG 22 x LMG
Ligand OEC 2 x OEC
Ligand FE2 2 x FE2
Ligand BCR 24 x BCR
Ligand LMT 14 x LMT
Ligand BCT 2 x BCT
Ligand CL 2 x CL
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLAC LCLS BEAMLINE CXI
Spacegroup: P212121
Unit cell:
a: 130.783Å b: 227.764Å c: 308.63Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.367 0.366 0.385

Quick links

Citations

21 review citations

The Structure of Photosystem II and the Mechanism of Water Oxidation in Photosynthesis.
Shen JR. (2015)
20 more

4 mentions without citation

Biophysical highlights from 54 years of macromolecular crystallography.
Richardson et al. (2014)
3 more