› 4yuu

X-ray diffraction
2.77Å resolution

Crystal structure of oxygen-evolving photosystem II from a red alga

Released:
DOI: 10.2210/pdb4yuu/pdb
PDB entry 4yuu coloured by chain, front view.
PDB entry 4yuu coloured by chain, side view.
PDB entry 4yuu coloured by chain, top view.
Source organism: Cyanidium caldarium
Primary publication:
Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga.
Ago H, Adachi H, Umena Y, Tashiro T, Kawakami K, Kamiya N, Tian L, Han G, Kuang T, Liu Z, Wang F, Zou H, Enami I, Miyano M, Shen JR
J Biol Chem 291 5676-5687 (2016)
PMID: 26757821

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

Assemblies composition:
hetero icosamer
hetero 21-mer (preferred)
hetero 22-mer
Assembly name:
PDBe Complex ID:
PDB-CPX-219120 (preferred)
Entry contents:
22 distinct polypeptide molecules
Macromolecules (22 distinct):
Photosystem II protein D1 Chains: A1, A2, a1, a2
Molecule details ›
Chains: A1, A2, a1, a2
Length: 344 amino acids
Theoretical weight: 38.07 KDa
Source organism: Cyanidium caldarium
UniProt:
  • Canonical: O19895 (Residues: 1-344; Coverage: 96%)
Gene name: psbA
Sequence domains: Photosynthetic reaction centre protein
Photosystem II CP47 reaction center protein Chains: B1, B2, b1, b2
Molecule details ›
Chains: B1, B2, b1, b2
Length: 509 amino acids
Theoretical weight: 56.62 KDa
Source organism: Cyanidium caldarium
UniProt:
  • Canonical: O19928 (Residues: 1-509; Coverage: 100%)
Gene name: psbB
Sequence domains: Photosystem II protein
Photosystem II CP43 reaction center protein Chains: C1, C2, c1, c2
Molecule details ›
Chains: C1, C2, c1, c2
Length: 460 amino acids
Theoretical weight: 50.52 KDa
Source organism: Cyanidium caldarium
UniProt:
  • Canonical: Q9TM46 (Residues: 1-460; Coverage: 100%)
Gene name: psbC
Sequence domains: Photosystem II protein
Photosystem II D2 protein Chains: D1, D2, d1, d2
Molecule details ›
Chains: D1, D2, d1, d2
Length: 351 amino acids
Theoretical weight: 39.34 KDa
Source organism: Cyanidium caldarium
UniProt:
  • Canonical: Q9TM47 (Residues: 1-351; Coverage: 100%)
Gene name: psbD
Sequence domains: Photosynthetic reaction centre protein
Cytochrome b559 subunit alpha Chains: E1, E2, e1, e2
Molecule details ›
Chains: E1, E2, e1, e2
Length: 84 amino acids
Theoretical weight: 9.53 KDa
Source organism: Cyanidium caldarium
UniProt:
  • Canonical: Q9TM20 (Residues: 1-84; Coverage: 100%)
Gene name: psbE
Sequence domains:
Cytochrome b559 subunit beta Chains: F1, F2, f1, f2
Molecule details ›
Chains: F1, F2, f1, f2
Length: 43 amino acids
Theoretical weight: 4.96 KDa
Source organism: Cyanidium caldarium
UniProt:
  • Canonical: Q9TM21 (Residues: 1-43; Coverage: 100%)
Gene name: psbF
Sequence domains: Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits
Photosystem II reaction center protein H Chains: H1, H2, h1, h2
Molecule details ›
Chains: H1, H2, h1, h2
Length: 67 amino acids
Theoretical weight: 7.5 KDa
Source organism: Cyanidium caldarium
UniProt:
  • Canonical: O19925 (Residues: 1-67; Coverage: 100%)
Gene name: psbH
Sequence domains: Photosystem II 10 kDa phosphoprotein
Photosystem II reaction center protein I Chains: I1, I2, i1, i2
Molecule details ›
Chains: I1, I2, i1, i2
Length: 38 amino acids
Theoretical weight: 4.47 KDa
Source organism: Cyanidium caldarium
UniProt:
  • Canonical: O19882 (Residues: 1-38; Coverage: 100%)
Gene name: psbI
Sequence domains: Photosystem II reaction centre I protein (PSII 4.8 kDa protein)
Photosystem II reaction center protein J Chains: J1, J2, j1, j2
Molecule details ›
Chains: J1, J2, j1, j2
Length: 39 amino acids
Theoretical weight: 4.09 KDa
Source organism: Cyanidium caldarium
UniProt:
  • Canonical: Q9TM23 (Residues: 1-39; Coverage: 100%)
Gene name: psbJ
Sequence domains: PsbJ
Photosystem II reaction center protein K Chains: K1, K2, k1, k2
Molecule details ›
Chains: K1, K2, k1, k2
Length: 41 amino acids
Theoretical weight: 4.7 KDa
Source organism: Cyanidium caldarium
UniProt:
  • Canonical: Q9TLR0 (Residues: 1-41; Coverage: 100%)
Gene name: psbK
Sequence domains: Photosystem II 4 kDa reaction centre component
Photosystem II reaction center protein L Chains: L1, L2, l1, l2
Molecule details ›
Chains: L1, L2, l1, l2
Length: 38 amino acids
Theoretical weight: 4.38 KDa
Source organism: Cyanidium caldarium
UniProt:
  • Canonical: Q9TM22 (Residues: 1-38; Coverage: 100%)
Gene name: psbL
Sequence domains: PsbL protein
PHOTOSYSTEM II REACTION CENTER PROTEIN M Chains: M1, M2, m1, m2
Molecule details ›
Chains: M1, M2, m1, m2
Length: 108 amino acids
Theoretical weight: 11.76 KDa
Source organism: Cyanidium caldarium
PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO Chains: O1, O2, o1, o2
Molecule details ›
Chains: O1, O2, o1, o2
Length: 329 amino acids
Theoretical weight: 35.5 KDa
Source organism: Cyanidium caldarium
Photosystem II reaction center protein T Chains: T1, T2, t1, t2
Molecule details ›
Chains: T1, T2, t1, t2
Length: 32 amino acids
Theoretical weight: 3.73 KDa
Source organism: Cyanidium caldarium
UniProt:
  • Canonical: O19927 (Residues: 1-32; Coverage: 100%)
Gene name: psbT
Sequence domains: Photosystem II reaction centre T protein
Photosystem II extrinsic protein U, chloroplastic Chains: U1, U2, u1, u2
Molecule details ›
Chains: U1, U2, u1, u2
Length: 155 amino acids
Theoretical weight: 16.87 KDa
Source organism: Cyanidium caldarium
UniProt:
  • Canonical: Q9ZQS5 (Residues: 1-154; Coverage: 100%)
Gene name: psbU
Sequence domains: Photosystem II 12 kDa extrinsic protein (PsbU)
Photosystem II extrinsic protein V Chains: V1, V2, v1, v2
Molecule details ›
Chains: V1, V2, v1, v2
Length: 155 amino acids
Theoretical weight: 17.24 KDa
Source organism: Cyanidium caldarium
UniProt:
  • Canonical: Q76FB0 (Residues: 1-155; Coverage: 100%)
Gene name: psbV
Sequence domains: Cytochrome c-550 domain
Photosystem II reaction center protein Psb30 Chains: Y1, Y2, y1, y2
Molecule details ›
Chains: Y1, Y2, y1, y2
Length: 35 amino acids
Theoretical weight: 4.04 KDa
Source organism: Cyanidium caldarium
UniProt:
  • Canonical: Q9TLX0 (Residues: 1-35; Coverage: 100%)
Gene names: psb30, ycf12, ycf34
Sequence domains: Photosystem II complex subunit Ycf12
PHOTOSYSTEM II REACTION CENTER PROTEIN X Chains: X1, X2, x1, x2
Molecule details ›
Chains: X1, X2, x1, x2
Length: 40 amino acids
Theoretical weight: 4.59 KDa
Source organism: Cyanidium caldarium
PEPTIDE CHAIN UNASSIGNED Chains: S1, S2, s1, s2
Molecule details ›
Chains: S1, S2, s1, s2
Length: 46 amino acids
Theoretical weight: 4.3 KDa
Source organism: Cyanidium caldarium
PEPTIDE CHAIN UNASSIGNED Chains: W1, W2, w1, w2
Molecule details ›
Chains: W1, W2, w1, w2
Length: 25 amino acids
Theoretical weight: 2.31 KDa
Source organism: Cyanidium caldarium
Extrinsic protein in photosystem II Chains: Q2, q1
Molecule details ›
Chains: Q2, q1
Length: 218 amino acids
Theoretical weight: 24.06 KDa
Source organism: Cyanidium caldarium
UniProt:
  • Canonical: Q76B86 (Residues: 1-218; Coverage: 100%)
Gene name: psbQ'
Sequence domains: Oxygen evolving enhancer protein 3 (PsbQ)
Photosystem II reaction center protein Z Chains: Z2, z2
Molecule details ›
Chains: Z2, z2
Length: 62 amino acids
Theoretical weight: 6.48 KDa
Source organism: Cyanidium caldarium

Ligands and Environments


Cofactor: Ligand HEM 8 x HEM
16 bound ligands:
Ligand BCR 38 x BCR
Ligand CL 4 x CL
Ligand CLA 140 x CLA
Ligand OEX 4 x OEX
Ligand PHO 8 x PHO
Ligand UNL 52 x UNL
Ligand LMG 25 x LMG
Ligand FE 4 x FE
Ligand BCT 4 x BCT
Ligand GOL 9 x GOL
Ligand LHG 19 x LHG
Ligand DGD 14 x DGD
Ligand LMT 14 x LMT
Ligand PL9 4 x PL9
Ligand SQD 4 x SQD
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 210.445Å b: 240.31Å c: 300.063Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.251 0.249 0.278

Quick links

Citations

7 review citations

Photosynthetic fuel for heterologous enzymes: the role of electron carrier proteins.
Mellor et al. (2017)
6 more

15 mentions without citation

Structural basis of light-harvesting in the photosystem II core complex.
Müh et al. (2020)
14 more