› 7oui

Electron Microscopy
2.79Å resolution

Structure of C2S2M2-type Photosystem supercomplex from Arabidopsis thaliana (digitonin-extracted)

Released:
DOI: 10.2210/pdb7oui/pdb
PDB entry 7oui coloured by chain, front view.
PDB entry 7oui coloured by chain, side view.
PDB entry 7oui coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction.
Graça AT, Hall M, Persson K, Schröder WP
OpenAccess logo Sci Rep 11 15534 (2021)
PMID: 34330992
Related structures: EMD-13078

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 52-mer (preferred)
PDBe Complex ID:
PDB-CPX-105836 (preferred)
Entry contents:
23 distinct polypeptide molecules
Macromolecules (23 distinct):
Chlorophyll a-b binding protein, chloroplastic Chains: 1, 3, 5, 7
Molecule details ›
Chains: 1, 3, 5, 7
Length: 266 amino acids
Theoretical weight: 28.19 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q39142 (Residues: 1-266; Coverage: 100%)
Gene names: At2g34430, F13P17.29, LHB1B1, LHCB1.4, Lhb1B1
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein 3, chloroplastic Chains: 2, 6
Molecule details ›
Chains: 2, 6
Length: 243 amino acids
Theoretical weight: 26.45 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9S7M0 (Residues: 23-265; Coverage: 92%)
Gene names: At5g54270, LHCB3, MDK4.9
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chains: 4, 8
Molecule details ›
Chains: 4, 8
Length: 212 amino acids
Theoretical weight: 23.2 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q9LMQ2 (Residues: 47-258; Coverage: 82%)
Gene names: At1g15820, At1g15820/F7H2.16, CHLOROPHYLL PROTEIN 24, CP24, F7H2.16, F7H2_16, LHCB6
Sequence domains: Chlorophyll A-B binding protein
Photosystem II protein D1 Chains: A, a
Molecule details ›
Chains: A, a
Length: 352 amino acids
Theoretical weight: 38.83 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P83755 (Residues: 2-353; Coverage: 100%)
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: 508 amino acids
Theoretical weight: 56.09 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P56777 (Residues: 1-508; 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)
(thale cress) hypothetical protein Chains: X, x
Molecule details ›
Chains: X, x
Length: 42 amino acids
Theoretical weight: 4.19 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: A0A7G2E9B1 (Residues: 314-355; Coverage: 12%)
Gene name: AT9943_LOCUS6465
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 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: G, N, Y, g, n, y
Molecule details ›
Chains: G, N, Y, g, n, y
Length: 232 amino acids
Theoretical weight: 24.89 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: P04778 (Residues: 36-267; Coverage: 87%)
Gene names: AB140, At1g29930, CAB1, F1N18.3, LHCB1.3
Sequence domains: Chlorophyll A-B binding protein
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
Photosystem II 5 kDa protein, chloroplastic Chains: U, u
Molecule details ›
Chains: U, u
Length: 28 amino acids
Theoretical weight: 3.18 KDa
Source organism: Arabidopsis thaliana
UniProt:
  • Canonical: Q39195 (Residues: 76-103; Coverage: 27%)
Gene names: At3g21055, MSA6.9, PSBT

Ligands and Environments


Cofactor: Ligand HEM 2 x HEM
17 bound ligands:
Ligand CHL 60 x CHL
Ligand CLA 162 x CLA
Ligand LHG 30 x LHG
Ligand PHO 4 x PHO
Ligand BCR 22 x BCR
Ligand SQD 8 x SQD
Ligand LMG 12 x LMG
Ligand PL9 4 x PL9
Ligand AJP 22 x AJP
Ligand BCT 2 x BCT
Ligand FE2 2 x FE2
Ligand DGD 8 x DGD
Ligand CA 4 x CA
Ligand CL 2 x CL
Ligand LUT 18 x LUT
Ligand NEX 10 x NEX
Ligand XAT 2 x XAT
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.79Å
Relevant EMDB volumes: EMD-13078

Quick links

Citations

4 review citations

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

2 mentions without citation

New Structural and Mechanistic Insights Into Functional Roles of Cytochrome b 559 in Photosystem II.
Chiu et al. (2022)
1 more