› 7dz8

Electron Microscopy
3.16Å resolution

State transition supercomplex PSI-LHCI-LHCII from the LhcbM1 lacking mutant of Chlamydomonas reinhardtii

Released:
DOI: 10.2210/pdb7dz8/pdb
PDB entry 7dz8 coloured by chain, front view.
PDB entry 7dz8 coloured by chain, side view.
PDB entry 7dz8 coloured by chain, top view.
Source organism: Chlamydomonas reinhardtii
Primary publication:
Structural basis of LhcbM5-mediated state transitions in green algae.
Pan X, Tokutsu R, Li A, Takizawa K, Song C, Murata K, Yamasaki T, Liu Z, Minagawa J, Li M
Nat Plants 7 1119-1131 (2021)
PMID: 34239095
Related structures: EMD-30926

Function and Biology Details

Reaction catalysed: 
Reduced plastocyanin + oxidized ferredoxin + light = oxidized plastocyanin + reduced ferredoxin
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 29-mer (preferred)
PDBe Complex ID:
PDB-CPX-108665 (preferred)
Entry contents:
25 distinct polypeptide molecules
Macromolecules (25 distinct):
Photosystem I P700 chlorophyll a apoprotein A1 Chain: A
Molecule details ›
Chain: A
Length: 751 amino acids
Theoretical weight: 83.24 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P12154 (Residues: 1-751; Coverage: 100%)
Gene names: ps1a1, psaA
Sequence domains: Photosystem I psaA/psaB protein
Photosystem I P700 chlorophyll a apoprotein A2 Chain: B
Molecule details ›
Chain: B
Length: 735 amino acids
Theoretical weight: 82.18 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P09144 (Residues: 1-735; Coverage: 100%)
Gene names: ps1a2, psaB
Sequence domains: Photosystem I psaA/psaB protein
Photosystem I iron-sulfur center Chain: C
Molecule details ›
Chain: C
Length: 81 amino acids
Theoretical weight: 8.87 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q00914 (Residues: 1-81; Coverage: 100%)
Gene name: psaC
Sequence domains: 4Fe-4S dicluster domain
Photosystem I reaction center subunit II, chloroplastic Chain: D
Molecule details ›
Chain: D
Length: 196 amino acids
Theoretical weight: 21.37 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q39615 (Residues: 1-196; Coverage: 100%)
Gene name: psaD
Sequence domains: PsaD
Photosystem I reaction center subunit IV, chloroplastic Chain: E
Molecule details ›
Chain: E
Length: 97 amino acids
Theoretical weight: 10.79 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P12352 (Residues: 1-97; Coverage: 100%)
Gene name: PSAE
Sequence domains: Photosystem I reaction centre subunit IV / PsaE
Photosystem I reaction center subunit III, chloroplastic Chain: F
Molecule details ›
Chain: F
Length: 227 amino acids
Theoretical weight: 24.09 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P12356 (Residues: 1-227; Coverage: 100%)
Gene name: PSAF
Sequence domains: Photosystem I reaction centre subunit III
Photosystem I reaction center subunit V, chloroplastic Chain: G
Molecule details ›
Chain: G
Length: 126 amino acids
Theoretical weight: 13.24 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P14224 (Residues: 1-126; Coverage: 100%)
Gene name: PSAG
Sequence domains: Photosystem I psaG / psaK
Photosystem I reaction center subunit VI, chloroplastic Chain: H
Molecule details ›
Chain: H
Length: 130 amino acids
Theoretical weight: 14.17 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P13352 (Residues: 1-130; Coverage: 100%)
Gene name: PSAH
Sequence domains: Photosystem I reaction centre subunit VI
Photosystem I reaction center subunit VIII Chain: I
Molecule details ›
Chain: I
Length: 106 amino acids
Theoretical weight: 10.59 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8IFG7 (Residues: 1-106; Coverage: 100%)
Gene name: CHLRE_03g165100v5
Sequence domains: Photosystem I reaction centre subunit VIII
Photosystem I reaction center subunit IX Chain: J
Molecule details ›
Chain: J
Length: 41 amino acids
Theoretical weight: 4.75 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P59777 (Residues: 1-41; Coverage: 100%)
Gene name: psaJ
Sequence domains: Photosystem I reaction centre subunit IX / PsaJ
Photosystem I reaction center subunit psaK, chloroplastic Chain: K
Molecule details ›
Chain: K
Length: 113 amino acids
Theoretical weight: 11.21 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P14225 (Residues: 1-113; Coverage: 100%)
Gene name: PSAK
Sequence domains: Photosystem I psaG / psaK
PSI subunit V Chain: L
Molecule details ›
Chain: L
Length: 196 amino acids
Theoretical weight: 20.3 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8IL32 (Residues: 1-196; Coverage: 100%)
Gene name: CHLRE_12g486300v5
Sequence domains: Photosystem I reaction centre subunit XI
Photosystem I subunit O Chain: O
Molecule details ›
Chain: O
Length: 126 amino acids
Theoretical weight: 13.75 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8JCL6 (Residues: 1-126; Coverage: 100%)
Gene name: CHLRE_07g334550v5
Chlorophyll a-b binding protein, chloroplastic Chains: 1, a
Molecule details ›
Chains: 1, a
Length: 228 amino acids
Theoretical weight: 23.92 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q05093 (Residues: 1-228; Coverage: 100%)
Gene names: CHLRE_06g283050v5, LhcI-6, Lhca1
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chain: 2
Molecule details ›
Chain: 2
Length: 246 amino acids
Theoretical weight: 26.95 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8IKC8 (Residues: 1-246; Coverage: 100%)
Gene name: CHLRE_12g508750v5
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chain: 3
Molecule details ›
Chain: 3
Length: 298 amino acids
Theoretical weight: 32.63 KDa
Source organism: Chlamydomonas reinhardtii
Chlorophyll a-b binding protein, chloroplastic Chain: 4
Molecule details ›
Chain: 4
Length: 264 amino acids
Theoretical weight: 28.73 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q75VZ0 (Residues: 1-264; Coverage: 100%)
Gene names: CHLRE_10g452050v5, LhcI-1
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chain: 5
Molecule details ›
Chain: 5
Length: 257 amino acids
Theoretical weight: 28.26 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q75VY8 (Residues: 1-257; Coverage: 100%)
Gene names: CHLRE_10g425900v5, LhcI-3
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chain: 6
Molecule details ›
Chain: 6
Length: 257 amino acids
Theoretical weight: 27.81 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q75VY6 (Residues: 1-257; Coverage: 100%)
Gene names: CHLRE_06g278213v5, LhcI-5
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chain: 7
Molecule details ›
Chain: 7
Length: 241 amino acids
Theoretical weight: 26.25 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q84Y02 (Residues: 1-241; Coverage: 100%)
Gene names: CHLRE_16g687900v5, Lhca
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chain: 8
Molecule details ›
Chain: 8
Length: 243 amino acids
Theoretical weight: 25.95 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q75VY7 (Residues: 1-243; Coverage: 100%)
Gene names: CHLRE_06g272650v5, LhcI-4
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chain: 9
Molecule details ›
Chain: 9
Length: 213 amino acids
Theoretical weight: 22.87 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8ITV3 (Residues: 1-213; Coverage: 100%)
Gene name: CHLRE_07g344950v5
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chains: W, X
Molecule details ›
Chains: W, X
Length: 249 amino acids
Theoretical weight: 26.68 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q93WE0 (Residues: 1-249; Coverage: 100%)
Gene names: CHLRE_12g548400v5, LhcII-3
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chains: U, Y, Z
Molecule details ›
Chains: U, Y, Z
Length: 257 amino acids
Theoretical weight: 27.41 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q93WL4 (Residues: 1-257; Coverage: 100%)
Gene names: CHLRE_04g232104v5, LhcII-1.3
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chain: V
Molecule details ›
Chain: V
Length: 268 amino acids
Theoretical weight: 28.8 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q9ZSJ4 (Residues: 1-268; Coverage: 100%)
Gene names: CHLRE_03g156900v5, Lhcb3
Sequence domains: Chlorophyll A-B binding protein

Ligands and Environments

12 bound ligands:
Ligand CLA 298 x CLA
Ligand PQN 2 x PQN
Ligand LHG 27 x LHG
Ligand BCR 40 x BCR
Ligand SF4 3 x SF4
Ligand LMU 7 x LMU
Ligand LMG 11 x LMG
Ligand DGD 1 x DGD
Ligand LUT 22 x LUT
Ligand XAT 16 x XAT
Ligand NEX 8 x NEX
Ligand CHL 36 x CHL
1 modified residue:
Ligand TPO 1 x TPO

Experiments and Validation Details

Entry percentile scores
Resolution: 3.16Å
Relevant EMDB volumes: EMD-30926

Quick links

Citations

4 review citations

Diversity Among Cyanobacterial Photosystem I Oligomers.
Chen et al. (2021)
3 more

1 mention without citation

Algal photosystem I dimer and high-resolution model of PSI-plastocyanin complex.
Naschberger et al. (2022)