› 1izl

X-ray diffraction
3.7Å resolution

Crystal Structure of Photosystem II

Released:
DOI: 10.2210/pdb1izl/pdb
PDB entry 1izl coloured by chain, front view.
PDB entry 1izl coloured by chain, side view.
PDB entry 1izl coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of oxygen-evolving photosystem II from Thermosynechococcus vulcanus at 3.7-A resolution.
Kamiya N, Shen JR
Proc Natl Acad Sci U S A 100 98-103 (2003)
PMID: 12518057

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 domain:

Structure analysis Details

Assembly composition:
hetero 28-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141190 (preferred)
Entry contents:
14 distinct polypeptide molecules
Macromolecules (14 distinct):
Photosystem II protein D1 Chains: A, J
Molecule details ›
Chains: A, J
Length: 360 amino acids
Theoretical weight: 39.79 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P51765 (Residues: 1-360; Coverage: 100%)
Gene names: psbA, psbA-1
Sequence domains: Photosynthetic reaction centre protein
Photosystem II CP47 reaction center protein Chains: B, L
Molecule details ›
Chains: B, L
Length: 472 amino acids
Theoretical weight: 49.48 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DIQ1 (Residues: 1-510; Coverage: 93%)
Gene names: psbB, tlr1530
Sequence domains: Photosystem II protein
Photosystem II CP43 reaction center protein Chains: C, M
Molecule details ›
Chains: C, M
Length: 473 amino acids
Theoretical weight: 49.87 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, N
Molecule details ›
Chains: D, N
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, P
Molecule details ›
Chains: E, P
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, Q
Molecule details ›
Chains: F, Q
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: Subunit PsbG Chains: G, R
Molecule details ›
Chains: G, R
Length: 220 amino acids
Theoretical weight: 18.74 KDa
Source organism: Thermosynechococcus vestitus BP-1
Photosystem II: Subunit PsbH Chains: H, S
Molecule details ›
Chains: H, S
Length: 33 amino acids
Theoretical weight: 2.83 KDa
Source organism: Thermosynechococcus vestitus BP-1
Photosystem II: Subunit PsbI Chains: I, T
Molecule details ›
Chains: I, T
Length: 26 amino acids
Theoretical weight: 2.23 KDa
Source organism: Thermosynechococcus vestitus BP-1
Photosystem II reaction center protein K Chains: K, W
Molecule details ›
Chains: K, W
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: Subunit PsbO Chains: O, Y
Molecule details ›
Chains: O, Y
Length: 205 amino acids
Theoretical weight: 17.46 KDa
Source organism: Thermosynechococcus vestitus BP-1
Photosystem II: Subunit PsbU Chains: U, Z
Molecule details ›
Chains: U, Z
Length: 97 amino acids
Theoretical weight: 8.27 KDa
Source organism: Thermosynechococcus vestitus BP-1
Photosystem II extrinsic protein V Chains: 0, V
Molecule details ›
Chains: 0, 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
Structure domains: Cytochrome c-like domain
Photosystem II: Subunit PsbX Chains: 1, X
Molecule details ›
Chains: 1, X
Length: 25 amino acids
Theoretical weight: 2.15 KDa
Source organism: Thermosynechococcus vestitus BP-1

Ligands and Environments


Cofactor: Ligand HEM 4 x HEM
6 bound ligands:
Ligand MN 8 x MN
Ligand CLA 72 x CLA
Ligand PHO 4 x PHO
Ligand FE 2 x FE
Ligand PLA 2 x PLA
Ligand BCR 2 x BCR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 129.377Å b: 225.192Å c: 308.672Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.53 0.53 not available

Quick links

Citations

107 review citations

Structure and function of photosystems I and II.
Nelson et al. (2006)
106 more

9 mentions without citation

Functional Mechanism of the Efflux Pumps Transcription Regulators From Pseudomonas aeruginosa Based on 3D Structures.
Housseini B Issa et al. (2018)
8 more