› 3a0b

X-ray diffraction
3.7Å resolution

Crystal structure of Br-substituted Photosystem II complex

Released:
DOI: 10.2210/pdb3a0b/pdb
PDB entry 3a0b coloured by chain, front view.
PDB entry 3a0b coloured by chain, side view.
PDB entry 3a0b coloured by chain, top view.
Source organism: Thermostichus vulcanus
Primary publication:
Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography.
Kawakami K, Umena Y, Kamiya N, Shen JR
Proc Natl Acad Sci U S A 106 8567-72 (2009)
PMID: 19433803

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-112072 (preferred)
Entry contents:
20 distinct polypeptide molecules
Macromolecules (20 distinct):
Photosystem II protein D1 Chains: A, a
Molecule details ›
Chains: A, a
Length: 344 amino acids
Theoretical weight: 38.3 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P51765 (Residues: 1-344; Coverage: 96%)
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: 488 amino acids
Theoretical weight: 54.04 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR1 (Residues: 1-488; Coverage: 97%)
Gene name: psbB
Sequence domains: Photosystem II protein
Structure domains: Photosystem II CP47 reaction center protein
Photosystem II CP43 reaction center protein Chains: C, c
Molecule details ›
Chains: C, c
Length: 447 amino acids
Theoretical weight: 48.76 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR7 (Residues: 5-451; Coverage: 99%)
Gene name: psbC
Sequence domains: Photosystem II protein
Structure domains: photosystem ii from thermosynechococcus elongatus
Photosystem II D2 protein Chains: D, d
Molecule details ›
Chains: D, d
Length: 340 amino acids
Theoretical weight: 38.12 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR8 (Residues: 3-342; Coverage: 99%)
Gene name: psbD
Sequence domains: Photosynthetic reaction centre protein
Cytochrome b559 subunit alpha Chains: E, e
Molecule details ›
Chains: E, e
Length: 83 amino acids
Theoretical weight: 9.48 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12238 (Residues: 2-84; Coverage: 99%)
Gene name: psbE
Sequence domains:
Structure domains: Photosystem II cytochrome b559, alpha subunit
Cytochrome b559 subunit beta Chains: F, f
Molecule details ›
Chains: F, f
Length: 44 amino acids
Theoretical weight: 4.94 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12239 (Residues: 2-45; Coverage: 98%)
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: 64 amino acids
Theoretical weight: 7.17 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P19052 (Residues: 1-64; Coverage: 99%)
Gene name: psbH
Sequence domains: Photosystem II 10 kDa phosphoprotein
Structure domains: Photosystem II reaction center protein H
Photosystem II reaction center protein I Chains: I, i
Molecule details ›
Chains: I, i
Length: 35 amino acids
Theoretical weight: 4.05 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12240 (Residues: 1-35; Coverage: 92%)
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: 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 Chains: K, k
Molecule details ›
Chains: K, k
Length: 36 amino acids
Theoretical weight: 3.89 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P19054 (Residues: 1-36; Coverage: 97%)
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: 36 amino acids
Theoretical weight: 4.02 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12312 (Residues: 1-36; Coverage: 100%)
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: 242 amino acids
Theoretical weight: 26.45 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR2 (Residues: 2-243; Coverage: 99%)
Gene name: psbO
Sequence domains: Manganese-stabilising protein / photosystem II polypeptide
Structure domains:
Photosystem II reaction center protein T Chains: T, t
Molecule details ›
Chains: T, t
Length: 30 amino acids
Theoretical weight: 3.62 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 Chains: U, u
Molecule details ›
Chains: U, u
Length: 98 amino acids
Theoretical weight: 11.1 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P56152 (Residues: 7-104; Coverage: 94%)
Gene name: psbU
Sequence domains: Photosystem II 12 kDa extrinsic protein (PsbU)
Structure domains: Photosystem II 12 kDa extrinsic protein
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
Structure domains: Cytochrome c-like domain
Photosystem II reaction center protein X Chains: X, x
Molecule details ›
Chains: X, x
Length: 34 amino acids
Theoretical weight: 3.48 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR4 (Residues: 1-34; Coverage: 85%)
Gene name: psbX
Sequence domains: Photosystem II reaction centre X protein (PsbX)
Photosystem II reaction center protein Psb30 Chains: Y, y
Molecule details ›
Chains: Y, y
Length: 28 amino acids
Theoretical weight: 3 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR3 (Residues: 3-30; Coverage: 93%)
Gene names: psb30, psbY, ycf12
Sequence domains: Photosystem II complex subunit Ycf12
Photosystem II reaction center protein Y Chains: N, n
Molecule details ›
Chains: N, n
Length: 24 amino acids
Theoretical weight: 2.06 KDa
Source organism: Thermostichus vulcanus
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
Structure domains: Photosystem II PsbZ, reaction centre

Ligands and Environments


Cofactor: Ligand HEM 4 x HEM
10 bound ligands:
Ligand OEC 2 x OEC
Ligand FE2 2 x FE2
Ligand CLA 70 x CLA
Ligand PHO 4 x PHO
Ligand PQ9 4 x PQ9
Ligand BCR 22 x BCR
Ligand LHG 2 x LHG
Ligand BR 4 x BR
Ligand MGE 8 x MGE
Ligand DGD 8 x DGD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 130.589Å b: 226.394Å c: 307.514Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.302 0.302 0.358

Quick links

Citations

20 review citations

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

4 mentions without citation

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance.
Enkavi et al. (2019)
3 more