› 6jlj

X-ray diffraction
2.15Å resolution

XFEL structure of cyanobacterial photosystem II (dark state, dataset1)

Released:
DOI: 10.2210/pdb6jlj/pdb
PDB entry 6jlj coloured by chain, front view.
PDB entry 6jlj coloured by chain, side view.
PDB entry 6jlj coloured by chain, top view.
Source organism: Thermostichus vulcanus
Primary publication:
An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser.
Suga M, Akita F, Yamashita K, Nakajima Y, Ueno G, Li H, Yamane T, Hirata K, Umena Y, Yonekura S, Yu LJ, Murakami H, Nomura T, Kimura T, Kubo M, Baba S, Kumasaka T, Tono K, Yabashi M, Isobe H, Yamaguchi K, Yamamoto M, Ago H, Shen JR
Science 366 334-338 (2019)
PMID: 31624207

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 39-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112070 (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
Photosystem II CP43 reaction center protein Chains: C, c
Molecule details ›
Chains: C, c
Length: 455 amino acids
Theoretical weight: 49.67 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR7 (Residues: 1-451; Coverage: 100%)
Gene name: psbC
Sequence domains: Photosystem II protein
Photosystem II D2 protein Chains: D, d
Molecule details ›
Chains: D, d
Length: 342 amino acids
Theoretical weight: 38.4 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR8 (Residues: 1-342; Coverage: 100%)
Gene name: psbD
Sequence domains: Photosynthetic reaction centre protein
Cytochrome b559 subunit alpha Chains: E, e
Molecule details ›
Chains: E, e
Length: 84 amino acids
Theoretical weight: 9.58 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12238 (Residues: 1-84; Coverage: 100%)
Gene name: psbE
Sequence domains:
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: 65 amino acids
Theoretical weight: 7.23 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P19052 (Residues: 1-65; Coverage: 100%)
Gene name: psbH
Sequence domains: Photosystem II 10 kDa phosphoprotein
Photosystem II reaction center protein I Chains: I, i
Molecule details ›
Chains: I, i
Length: 38 amino acids
Theoretical weight: 4.44 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12240 (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: J, j
Molecule details ›
Chains: J, j
Length: 39 amino acids
Theoretical weight: 3.97 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: Q7DGD4 (Residues: 2-40; Coverage: 98%)
Gene name: psbJ
Sequence domains: PsbJ
Photosystem II reaction center protein K Chains: K, k
Molecule details ›
Chains: K, k
Length: 37 amino acids
Theoretical weight: 4.1 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P19054 (Residues: 1-37; Coverage: 100%)
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: 4.01 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: 244 amino acids
Theoretical weight: 26.65 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR2 (Residues: 1-244; Coverage: 100%)
Gene name: psbO
Sequence domains: Manganese-stabilising protein / photosystem II polypeptide
Photosystem II reaction center protein T Chains: T, t
Molecule details ›
Chains: T, t
Length: 32 amino acids
Theoretical weight: 3.91 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12313 (Residues: 1-32; Coverage: 100%)
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: 104 amino acids
Theoretical weight: 11.66 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P56152 (Residues: 1-104; Coverage: 100%)
Gene name: psbU
Sequence domains: Photosystem II 12 kDa extrinsic protein (PsbU)
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
Photosystem II reaction center protein Psb30 Chains: Y, y
Molecule details ›
Chains: Y, y
Length: 30 amino acids
Theoretical weight: 3.23 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR3 (Residues: 1-30; Coverage: 100%)
Gene names: psb30, psbY, ycf12
Sequence domains: Photosystem II complex subunit Ycf12
Photosystem II reaction center protein X Chains: X, x
Molecule details ›
Chains: X, x
Length: 40 amino acids
Theoretical weight: 4.19 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR4 (Residues: 1-40; Coverage: 100%)
Gene name: psbX
Sequence domains: Photosystem II reaction centre X protein (PsbX)
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
Photosystem II reaction center protein Y Chain: R
Molecule details ›
Chain: R
Length: 34 amino acids
Theoretical weight: 3.86 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P0DM37 (Residues: 1-34; Coverage: 100%)
Gene name: psbY
Sequence domains: Photosystem II protein Y (PsbY)

Ligands and Environments


Cofactor: Ligand HEM 4 x HEM
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 35 x GOL
Ligand LMT 14 x LMT
Ligand OEX 2 x OEX
Ligand PL9 4 x PL9
Ligand UNL 18 x UNL
Ligand CA 9 x CA
Ligand HTG 17 x HTG
Ligand LMG 12 x LMG
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

Entry percentile scores
X-ray source: SACLA BEAMLINE BL3
Spacegroup: P212121
Unit cell:
a: 121.97Å b: 228.72Å c: 286.98Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.154 0.152 0.198

Quick links

Citations

15 review citations

Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient.
Kaur et al. (2021)
14 more

4 mentions without citation

Evolutionary diversity of proton and water channels on the oxidizing side of photosystem II and their relevance to function.
Hussein et al. (2023)
3 more