› 4ub6

X-ray diffraction
1.95Å resolution

Native structure of photosystem II (dataset-1) by a femtosecond X-ray laser

Released:
DOI: 10.2210/pdb4ub6/pdb
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PDB entry 4ub6 coloured by chain, front view.
PDB entry 4ub6 coloured by chain, side view.
PDB entry 4ub6 coloured by chain, top view.
Source organism: Thermostichus vulcanus
Primary publication:
Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses.
Suga M, Akita F, Hirata K, Ueno G, Murakami H, Nakajima Y, Shimizu T, Yamashita K, Yamamoto M, Ago H, Shen JR
Nature 517 99-103 (2015)
PMID: 25470056

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 (preferred)
hetero nonadecamer
Assembly name:
PDBe Complex ID:
PDB-CPX-112066 (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: 38.24 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: 505 amino acids
Theoretical weight: 56.07 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR1 (Residues: 1-505; Coverage: 100%)
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
Photosystem II D2 protein Chains: D, d
Cytochrome b559 subunit alpha Chains: E, e
Cytochrome b559 subunit beta Chains: F, f
Photosystem II reaction center protein H Chains: H, h
Photosystem II reaction center protein I Chains: I, i
Photosystem II reaction center protein J Chains: J, j
Photosystem II reaction center protein K Chains: K, k
Photosystem II reaction center protein L Chains: L, l
Photosystem II reaction center protein M Chains: M, m
Photosystem II extrinsic protein O Chains: O, o
Photosystem II reaction center protein T Chains: T, t
Photosystem II extrinsic protein U Chains: U, u
Photosystem II extrinsic protein V Chains: V, v
Photosystem II reaction center protein Psb30 Chains: Y, y
Photosystem II reaction center protein X Chains: X, x
Photosystem II reaction center protein Z Chains: Z, z
Photosystem II reaction center protein Y Chain: R

Ligands and Environments


Cofactor: Ligand HEM 2 x HEM

Cofactor: Ligand HEC 2 x HEC
18 bound ligands:
Ligand FE2 2 x FE2
Ligand CL 6 x CL
Ligand BCT 2 x BCT
Ligand CLA 70 x CLA
Ligand PHO 4 x PHO
Ligand BCR 22 x BCR
Ligand SQD 8 x SQD
Ligand GOL 37 x GOL
Ligand LMT 14 x LMT
Ligand OEX 2 x OEX
Ligand PL9 4 x PL9
Ligand UNL 18 x UNL
Ligand CA 7 x CA
Ligand LMG 12 x LMG
Ligand HTG 17 x HTG
Ligand DGD 10 x DGD
Ligand LHG 10 x LHG
Ligand MG 2 x MG
1 modified residue:
Ligand FME 6 x FME

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SACLA BEAMLINE BL3
Spacegroup: P212121
Unit cell:
a: 123.744Å b: 229.989Å c: 288.337Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.238

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Citations

67 review citations

Production of Reactive Oxygen Species by Photosystem II as a Response to Light and Temperature Stress.
Pospíšil P. (2016)
66 more

35 mentions without citation

Photoactivation: The Light-Driven Assembly of the Water Oxidation Complex of Photosystem II.
Bao et al. (2016)
34 more

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