› 8j6z

Electron Microscopy
2.79Å resolution

Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-LHCII-ST2)

Released:
DOI: 10.2210/pdb8j6z/pdb
PDB entry 8j6z coloured by chain, front view.
PDB entry 8j6z coloured by chain, side view.
PDB entry 8j6z coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Regulatory dynamics of the higher-plant PSI-LHCI supercomplex during state transitions.
Wu J, Chen S, Wang C, Lin W, Huang C, Fan C, Han D, Lu D, Xu X, Sui S, Zhang L
Mol Plant 16 1937-1950 (2023)
PMID: 37936349
Related structures: EMD-36021

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero icosamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-235784 (preferred)
Entry contents:
19 distinct polypeptide molecules
Macromolecules (19 distinct):
Chlorophyll a-b binding protein 6, chloroplastic Chain: 1
Molecule details ›
Chain: 1
Length: 241 amino acids
Theoretical weight: 26.02 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: Q01667 (Residues: 1-241; Coverage: 100%)
Gene names: At3g54890, CAB6, F28P10.130, LHCA1
Sequence domains: Chlorophyll A-B binding protein
Photosystem I chlorophyll a/b-binding protein 2, chloroplastic Chain: 2
Molecule details ›
Chain: 2
Length: 257 amino acids
Theoretical weight: 27.78 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SYW8 (Residues: 1-257; Coverage: 100%)
Gene names: At3g61470, F2A19.70, LHCA2
Sequence domains: Chlorophyll A-B binding protein
Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic Chain: 3
Molecule details ›
Chain: 3
Length: 273 amino acids
Theoretical weight: 29.21 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SY97 (Residues: 1-273; Coverage: 100%)
Gene names: At1g61520, LHCA3, T25B24.12
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein 4, chloroplastic Chain: 4
Molecule details ›
Chain: 4
Length: 251 amino acids
Theoretical weight: 27.76 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: P27521 (Residues: 1-251; Coverage: 100%)
Gene names: At3g47470, CAB4, F1P2.20, LHCA4
Sequence domains: Chlorophyll A-B binding protein
Photosystem I P700 chlorophyll a apoprotein A1 Chain: A
Molecule details ›
Chain: A
Length: 750 amino acids
Theoretical weight: 83.32 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: P56766 (Residues: 1-750; Coverage: 100%)
Gene names: AtCg00350, psaA
Sequence domains: Photosystem I psaA/psaB protein
Photosystem I P700 chlorophyll a apoprotein A2 Chain: B
Molecule details ›
Chain: B
Length: 734 amino acids
Theoretical weight: 82.56 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: P56767 (Residues: 1-734; Coverage: 100%)
Gene names: AtCg00340, 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: 9.05 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: P62090 (Residues: 1-81; Coverage: 100%)
Gene names: AtCg01060, frxA, psaC
Sequence domains: 4Fe-4S dicluster domain
Photosystem I reaction center subunit II-2, chloroplastic Chain: D
Molecule details ›
Chain: D
Length: 204 amino acids
Theoretical weight: 22.34 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SA56 (Residues: 1-204; Coverage: 100%)
Gene names: At1g03130, F10O3_4, PSAD2
Sequence domains: PsaD
Photosystem I reaction center subunit IV A, chloroplastic Chain: E
Molecule details ›
Chain: E
Length: 143 amino acids
Theoretical weight: 14.98 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: Q9S831 (Residues: 1-143; Coverage: 100%)
Gene names: At4g28750, F16A16.140, PSAE1
Sequence domains: Photosystem I reaction centre subunit IV / PsaE
Photosystem I reaction center subunit III, chloroplastic Chain: F
Molecule details ›
Chain: F
Length: 221 amino acids
Theoretical weight: 24.2 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SHE8 (Residues: 1-221; Coverage: 100%)
Gene names: At1g31330, PSAF, T19E23.12
Sequence domains: Photosystem I reaction centre subunit III
Photosystem I reaction center subunit V, chloroplastic Chain: G
Molecule details ›
Chain: G
Length: 160 amino acids
Theoretical weight: 17.1 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: Q9S7N7 (Residues: 1-160; Coverage: 100%)
Gene names: At1g55670, F20N2.21, F20N2.33, F20N2_3, PSAG
Sequence domains: Photosystem I psaG / psaK
Photosystem I reaction center subunit VI-2, chloroplastic Chain: H
Molecule details ›
Chain: H
Length: 145 amino acids
Theoretical weight: 15.29 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SUI6 (Residues: 1-145; Coverage: 100%)
Gene names: At1g52230, F9I5.11, PSAH2
Sequence domains: Photosystem I reaction centre subunit VI
Photosystem I reaction center subunit VIII Chain: I
Molecule details ›
Chain: I
Length: 37 amino acids
Theoretical weight: 4.14 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: P56768 (Residues: 1-37; Coverage: 100%)
Gene names: AtCg00510, psaI
Sequence domains: Photosystem I reaction centre subunit VIII
Photosystem I reaction center subunit IX Chain: J
Molecule details ›
Chain: J
Length: 44 amino acids
Theoretical weight: 5.01 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: P56769 (Residues: 1-44; Coverage: 100%)
Gene names: AtCg00630, psaJ
Sequence domains: Photosystem I reaction centre subunit IX / PsaJ
Photosystem I reaction center subunit psaK, chloroplastic Chain: K
Molecule details ›
Chain: K
Length: 130 amino acids
Theoretical weight: 13.22 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SUI5 (Residues: 1-130; Coverage: 100%)
Gene names: At1g30380, PSAK, T4K22.2
Sequence domains: Photosystem I psaG / psaK
Photosystem I reaction center subunit XI, chloroplastic Chain: L
Molecule details ›
Chain: L
Length: 219 amino acids
Theoretical weight: 23.07 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SUI4 (Residues: 1-219; Coverage: 100%)
Gene names: At4g12800, PSAL, T20K18.150
Sequence domains: Photosystem I reaction centre subunit XI
Photosystem I subunit O Chain: O
Molecule details ›
Chain: O
Length: 140 amino acids
Theoretical weight: 15.16 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: Q949Q5 (Residues: 1-140; Coverage: 100%)
Gene names: At1g08380, PSAO, T27G7
Sequence domains: PsaO transmembrane domain
Chlorophyll a-b binding protein 2, chloroplastic Chains: x, y
Molecule details ›
Chains: x, y
Length: 267 amino acids
Theoretical weight: 28.25 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: P0CJ48 (Residues: 1-267; Coverage: 100%)
Gene names: AB165, At1g29920, CAB2, F1N18.4, LHCB1.1, LHCP-B
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein 2.1, chloroplastic Chain: z
Molecule details ›
Chain: z
Length: 265 amino acids
Theoretical weight: 28.75 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
UniProt:
  • Canonical: Q9SHR7 (Residues: 1-265; Coverage: 100%)
Gene names: At2g05100, F15L11.2, LHCB2.1, LHCB2.3
Sequence domains: Chlorophyll A-B binding protein

Ligands and Environments

12 bound ligands:
Ligand CHL 30 x CHL
Ligand CLA 168 x CLA
Ligand XAT 6 x XAT
Ligand LHG 9 x LHG
Ligand LUT 11 x LUT
Ligand BCR 27 x BCR
Ligand LMG 2 x LMG
Ligand CL0 1 x CL0
Ligand SF4 3 x SF4
Ligand PQN 2 x PQN
Ligand DGD 1 x DGD
Ligand NEX 3 x NEX
1 modified residue:
Ligand TPO 1 x TPO

Experiments and Validation Details

Entry percentile scores
Resolution: 2.79Å
Relevant EMDB volumes: EMD-36021
Expression system: Arabidopsis thaliana

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