› 5mdx

Electron Microscopy
5.3Å resolution

Cryo-EM structure of the PSII supercomplex from Arabidopsis thaliana

Released:
DOI: 10.2210/pdb5mdx/pdb
PDB entry 5mdx coloured by chain, front view.
PDB entry 5mdx coloured by chain, side view.
PDB entry 5mdx coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Subunit and chlorophyll organization of the plant photosystem II supercomplex.
van Bezouwen LS, Caffarri S, Kale RS, KouĊ™il R, Thunnissen AWH, Oostergetel GT, Boekema EJ
Nat Plants 3 17080 (2017)
PMID: 28604725
Related structures: EMD-3491

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)
PDBe Complex ID:
PDB-CPX-138172 (preferred)
Entry contents:
20 distinct polypeptide molecules
Macromolecules (20 distinct):
Photosystem II protein D1 Chains: A, a
Molecule details ›
Chains: A, a
Length: 343 amino acids
Theoretical weight: 38 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P83755 (Residues: 2-344; Coverage: 97%)
Gene names: AtCg00020, psbA
Sequence domains: Photosynthetic reaction centre protein
Photosystem II CP47 reaction center protein Chains: B, b
Molecule details ›
Chains: B, b
Length: 507 amino acids
Theoretical weight: 55.96 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P56777 (Residues: 2-508; Coverage: 100%)
Gene names: AtCg00680, psbB
Sequence domains: Photosystem II protein
Photosystem II CP43 reaction center protein Chains: C, c
Molecule details ›
Chains: C, c
Length: 459 amino acids
Theoretical weight: 50.09 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P56778 (Residues: 15-473; Coverage: 97%)
Gene names: AtCg00280, CP43, psbC
Sequence domains: Photosystem II protein
Photosystem II D2 protein Chains: D, d
Molecule details ›
Chains: D, d
Length: 352 amino acids
Theoretical weight: 39.44 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P56761 (Residues: 2-353; Coverage: 100%)
Gene names: AtCg00270, 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: Arabidopsis thaliana
UniProt:
  • Canonical: P56779 (Residues: 1-83; Coverage: 100%)
Gene names: AtCg00580, psbE
Sequence domains:
Cytochrome b559 subunit beta Chains: F, f
Molecule details ›
Chains: F, f
Length: 39 amino acids
Theoretical weight: 4.43 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P62095 (Residues: 1-39; Coverage: 100%)
Gene names: AtCg00570, 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: 72 amino acids
Theoretical weight: 7.58 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P56780 (Residues: 2-73; Coverage: 99%)
Gene names: AtCg00710, psbH
Sequence domains: Photosystem II 10 kDa phosphoprotein
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: Arabidopsis thaliana
UniProt:
  • Canonical: P62100 (Residues: 1-36; Coverage: 100%)
Gene names: AtCg00080, psbI
Sequence domains: Photosystem II reaction centre I protein (PSII 4.8 kDa protein)
Photosystem II reaction center protein K Chains: K, k
Molecule details ›
Chains: K, k
Length: 37 amino acids
Theoretical weight: 4.24 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P56782 (Residues: 25-61; Coverage: 61%)
Gene names: AtCg00070, 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: 4.47 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P60129 (Residues: 1-38; Coverage: 100%)
Gene names: AtCg00560, 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: Arabidopsis thaliana
UniProt:
  • Canonical: P62109 (Residues: 1-34; Coverage: 100%)
Gene names: AtCg00220, psbM
Sequence domains: Photosystem II reaction centre M protein (PsbM)
Oxygen-evolving enhancer protein 1-1, chloroplastic Chains: O, o
Molecule details ›
Chains: O, o
Length: 247 amino acids
Theoretical weight: 26.59 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P23321 (Residues: 86-332; Coverage: 74%)
Gene names: At5g66570, K1F13.25, OEC33, PSBO, PSBO1
Sequence domains: Manganese-stabilising protein / photosystem II polypeptide
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: Arabidopsis thaliana
UniProt:
  • Canonical: P61839 (Residues: 1-33; Coverage: 100%)
Gene names: AtCg00690, psbT, ycf8
Sequence domains: Photosystem II reaction centre T protein
Photosystem II reaction center W protein, chloroplastic Chains: W, w
Molecule details ›
Chains: W, w
Length: 54 amino acids
Theoretical weight: 6.04 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q39194 (Residues: 80-133; Coverage: 41%)
Gene names: At2g30570, PSBW, T6B20.8
Sequence domains: Photosystem II reaction centre W protein (PsbW)
Expressed protein Chains: X, x
Molecule details ›
Chains: X, x
Length: 116 amino acids
Theoretical weight: 11.83 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SKI3 (Residues: 1-116; Coverage: 100%)
Gene names: At2g06520, At2g06520/T12H3.7, PSBX, PSII-X, T12H3.7, T12H3_7, photosystem II subunit X
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: 6.57 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P56790 (Residues: 1-62; Coverage: 100%)
Gene names: AtCg00300, psbZ, ycf9
Sequence domains: YCF9
Chlorophyll a-b binding protein CP29.1, chloroplastic Chains: R, r
Molecule details ›
Chains: R, r
Length: 250 amino acids
Theoretical weight: 27.3 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q07473 (Residues: 41-290; Coverage: 86%)
Gene names: At5g01530, F7A7_50, LHCB4.1
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein CP26, chloroplastic Chains: S, s
Molecule details ›
Chains: S, s
Length: 232 amino acids
Theoretical weight: 25.23 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9XF89 (Residues: 49-280; Coverage: 83%)
Gene names: At4g10340, F24G24.140, LHCB5
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein 1, chloroplastic Chains: 1, 2, 3, 5, 6, 7, G, N, Y, g, n, y
Molecule details ›
Chains: 1, 2, 3, 5, 6, 7, G, N, Y, g, n, y
Length: 224 amino acids
Theoretical weight: 23.97 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P04778 (Residues: 44-267; Coverage: 84%)
Gene names: AB140, At1g29930, CAB1, F1N18.3, LHCB1.3
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chains: 4, 8
Molecule details ›
Chains: 4, 8
Length: 210 amino acids
Theoretical weight: 23.01 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9LMQ2 (Residues: 48-257; Coverage: 81%)
Gene names: At1g15820, At1g15820/F7H2.16, CHLOROPHYLL PROTEIN 24, CP24, F7H2.16, F7H2_16, LHCB6
Sequence domains: Chlorophyll A-B binding protein

Ligands and Environments


Cofactor: Ligand HEM 2 x HEM
4 bound ligands:
Ligand FE2 2 x FE2
Ligand CLA 212 x CLA
Ligand PHO 4 x PHO
Ligand CHL 96 x CHL
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 5.3Å
Relevant EMDB volumes: EMD-3491

Quick links

Citations

5 review citations

Composition, phosphorylation and dynamic organization of photosynthetic protein complexes in plant thylakoid membrane.
Rantala et al. (2020)
4 more

13 mentions without citation

Here comes the sun: How optimization of photosynthetic light reactions can boost crop yields.
Walter et al. (2022)
12 more