› 3jcu

Electron Microscopy
3.2Å resolution

Cryo-EM structure of spinach PSII-LHCII supercomplex at 3.2 Angstrom resolution

Released:
DOI: 10.2210/pdb3jcu/pdb
PDB entry 3jcu coloured by chain, front view.
PDB entry 3jcu coloured by chain, side view.
PDB entry 3jcu coloured by chain, top view.
Source organism: Spinacia oleracea
Primary publication:
Structure of spinach photosystem II-LHCII supercomplex at 3.2 Å resolution.
Wei X, Su X, Cao P, Liu X, Chang W, Li M, Zhang X, Liu Z
Nature 534 69-74 (2016)
PMID: 27251276
Related structures: EMD-6617

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 50-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-236886 (preferred)
Entry contents:
23 distinct polypeptide molecules
Macromolecules (23 distinct):
Photosystem II protein D1 Chains: A, a
Molecule details ›
Chains: A, a
Length: 344 amino acids
Theoretical weight: 38.13 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P69560 (Residues: 1-344; Coverage: 98%)
Gene name: psbA
Sequence domains: Photosynthetic reaction centre protein
Photosystem II CP47 reaction center protein Chains: B, b
Molecule details ›
Chains: B, b
Length: 508 amino acids
Theoretical weight: 56.21 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P04160 (Residues: 1-508; 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
Molecule details ›
Chains: C, c
Length: 473 amino acids
Theoretical weight: 51.88 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P06003 (Residues: 1-473; Coverage: 100%)
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: 353 amino acids
Theoretical weight: 39.54 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P06005 (Residues: 1-353; Coverage: 100%)
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: 9.39 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P69383 (Residues: 1-83; Coverage: 100%)
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: 39 amino acids
Theoretical weight: 4.5 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P60128 (Residues: 1-39; Coverage: 100%)
Gene name: psbF
Sequence domains: Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits
Chlorophyll a-b binding protein, chloroplastic Chains: G, N, Y, g, n, y
Molecule details ›
Chains: G, N, Y, g, n, y
Length: 267 amino acids
Theoretical weight: 28.45 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P12333 (Residues: 1-267; Coverage: 100%)
Sequence domains: Chlorophyll A-B binding protein
Structure domains: Chlorophyll a/b binding protein domain
Photosystem II reaction center protein H Chains: H, h
Molecule details ›
Chains: H, h
Length: 73 amino acids
Theoretical weight: 7.74 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P05146 (Residues: 1-73; Coverage: 100%)
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: 36 amino acids
Theoretical weight: 4.17 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P62103 (Residues: 1-36; 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: 40 amino acids
Theoretical weight: 4.12 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q9M3L2 (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: 59 amino acids
Theoretical weight: 6.75 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P12163 (Residues: 1-59; 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: 38 amino acids
Theoretical weight: 4.5 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P60150 (Residues: 1-38; Coverage: 100%)
Gene name: psbL
Sequence domains: PsbL protein
Photosystem II reaction center protein M Chains: M, m
Molecule details ›
Chains: M, m
Length: 34 amino acids
Theoretical weight: 3.78 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P62112 (Residues: 1-34; Coverage: 100%)
Gene name: psbM
Sequence domains: Photosystem II reaction centre M protein (PsbM)
Oxygen-evolving enhancer protein 1, chloroplastic Chains: O, o
Molecule details ›
Chains: O, o
Length: 332 amino acids
Theoretical weight: 35.21 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P12359 (Residues: 1-332; Coverage: 100%)
Gene name: PSBO
Sequence domains: Manganese-stabilising protein / photosystem II polypeptide
Structure domains:
Oxygen-evolving enhancer protein 2, chloroplastic Chains: P, p
Molecule details ›
Chains: P, p
Length: 267 amino acids
Theoretical weight: 28.5 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P12302 (Residues: 1-267; Coverage: 100%)
Gene name: PSBP
Sequence domains:
Structure domains: Mog1/PsbP, alpha/beta/alpha sandwich
Oxygen-evolving enhancer protein 3, chloroplastic Chains: Q, q
Molecule details ›
Chains: Q, q
Length: 232 amino acids
Theoretical weight: 24.88 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P12301 (Residues: 1-232; Coverage: 100%)
Gene name: PSBQ
Sequence domains: Oxygen evolving enhancer protein 3 (PsbQ)
Structure domains: Oxygen-evolving enhancer protein 3 (PsbQ), four-helix up-down bundle
Chlorophyll a-b binding protein, chloroplastic Chains: R, r
Molecule details ›
Chains: R, r
Length: 243 amino acids
Theoretical weight: 26.74 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: F2Z293 (Residues: 1-243; Coverage: 100%)
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll A-B Binding protein 26 kD (CP26) Chains: S, s
Molecule details ›
Chains: S, s
Length: 295 amino acids
Theoretical weight: 31.34 KDa
Source organism: Spinacia oleracea
Structure domains: Chlorophyll a/b binding protein domain
Photosystem II reaction center protein T Chains: T, t
Molecule details ›
Chains: T, t
Length: 33 amino acids
Theoretical weight: 3.83 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P61840 (Residues: 1-33; Coverage: 100%)
Gene names: psbT, ycf8
Sequence domains: Photosystem II reaction centre T protein
Photosystem II Reaction Center Tn protein Chains: U, u
Molecule details ›
Chains: U, u
Length: 99 amino acids
Theoretical weight: 10.68 KDa
Source organism: Spinacia oleracea
Photosystem II reaction center W protein, chloroplastic Chains: W, w
Molecule details ›
Chains: W, w
Length: 137 amino acids
Theoretical weight: 14.19 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q41387 (Residues: 1-137; Coverage: 100%)
Gene name: psbW
Sequence domains: Photosystem II reaction centre W protein (PsbW)
Photosystem II Reaction Center X protein Chains: X, x
Molecule details ›
Chains: X, x
Length: 117 amino acids
Theoretical weight: 11.96 KDa
Source organism: Spinacia oleracea
Photosystem II reaction center protein Z Chains: Z, z
Molecule details ›
Chains: Z, z
Length: 62 amino acids
Theoretical weight: 6.54 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q9M3M6 (Residues: 1-62; Coverage: 100%)
Gene names: psbZ, ycf9
Sequence domains: YCF9
Structure domains: Photosystem II PsbZ, reaction centre

Ligands and Environments


Cofactor: Ligand HEM 2 x HEM
16 bound ligands:
Ligand OEX 2 x OEX
Ligand FE2 2 x FE2
Ligand CL 4 x CL
Ligand CLA 156 x CLA
Ligand PHO 4 x PHO
Ligand BCR 20 x BCR
Ligand SQD 6 x SQD
Ligand LMG 10 x LMG
Ligand DGD 8 x DGD
Ligand BCT 2 x BCT
Ligand PL9 2 x PL9
Ligand LHG 18 x LHG
Ligand CHL 50 x CHL
Ligand LUT 18 x LUT
Ligand XAT 8 x XAT
Ligand NEX 10 x NEX
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-6617

Quick links

Citations

27 review citations

Unravelling biological macromolecules with cryo-electron microscopy.
Fernandez-Leiro et al. (2016)
26 more

33 mentions without citation

Photosynthesis.
Johnson MP. (2016)
32 more