› 5l8r

X-ray diffraction
2.6Å resolution

The structure of plant photosystem I super-complex at 2.6 angstrom resolution.

Released:
DOI: 10.2210/pdb5l8r/pdb
PDB entry 5l8r coloured by chain, front view.
PDB entry 5l8r coloured by chain, side view.
PDB entry 5l8r coloured by chain, top view.
Source organism: Pisum sativum
Primary publication:
Structure of the plant photosystem I supercomplex at 2.6 Å resolution.
Mazor Y, Borovikova A, Caspy I, Nelson N
Nat Plants 3 17014 (2017)
PMID: 28248295

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 hexadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-101280 (preferred)
Entry contents:
16 distinct polypeptide molecules
Macromolecules (16 distinct):
Chlorophyll a-b binding protein, chloroplastic Chain: 1
Molecule details ›
Chain: 1
Length: 193 amino acids
Theoretical weight: 21.34 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9L2 (Residues: 1-170; Coverage: 100%)
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chain: 2
Molecule details ›
Chain: 2
Length: 269 amino acids
Theoretical weight: 28.91 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q41038 (Residues: 1-269; Coverage: 100%)
Gene names: KIW84_045602, lhaB
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein 3, chloroplastic Chain: 3
Molecule details ›
Chain: 3
Length: 275 amino acids
Theoretical weight: 29.63 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q32904 (Residues: 1-275; Coverage: 100%)
Gene name: lhca3
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein P4, chloroplastic Chain: 4
Molecule details ›
Chain: 4
Length: 198 amino acids
Theoretical weight: 21.99 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q9SQL2 (Residues: 52-249; Coverage: 79%)
Gene name: lhcA-P4
Sequence domains: Chlorophyll A-B binding protein
Photosystem I P700 chlorophyll a apoprotein A1 Chain: A
Molecule details ›
Chain: A
Length: 758 amino acids
Theoretical weight: 84.27 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P05310 (Residues: 1-758; Coverage: 100%)
Gene names: psaA, psaA1
Sequence domains: Photosystem I psaA/psaB protein
Structure domains: Photosystem I PsaA/PsaB
Photosystem I P700 chlorophyll a apoprotein A2 Chain: B
Molecule details ›
Chain: B
Length: 734 amino acids
Theoretical weight: 82.51 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: A0A0F6NGI2 (Residues: 1-734; Coverage: 100%)
Gene name: psaB
Sequence domains: Photosystem I psaA/psaB protein
Structure domains: Photosystem I PsaA/PsaB
Photosystem I iron-sulfur center Chain: C
Molecule details ›
Chain: C
Length: 81 amino acids
Theoretical weight: 8.99 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P10793 (Residues: 1-81; Coverage: 100%)
Gene names: frxA, psaC
Sequence domains: 4Fe-4S dicluster domain
Structure domains: Alpha-Beta Plaits
Photosystem I reaction center subunit II, chloroplastic Chain: D
Molecule details ›
Chain: D
Length: 143 amino acids
Theoretical weight: 16.04 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9K8 (Residues: 1-138; Coverage: 100%)
Sequence domains: PsaD
Structure domains: Photosystem I PsaD, reaction center subunit II
Photosystem I reaction center subunit IV Chain: E
Molecule details ›
Chain: E
Length: 66 amino acids
Theoretical weight: 7.48 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9K6 (Residues: 1-64; Coverage: 100%)
Sequence domains: Photosystem I reaction centre subunit IV / PsaE
Structure domains: SH3 type barrels.
Photosystem I reaction center subunit III Chain: F
Molecule details ›
Chain: F
Length: 154 amino acids
Theoretical weight: 17.24 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: A0A0M3KL12 (Residues: 1-154; Coverage: 100%)
Sequence domains: Photosystem I reaction centre subunit III
Structure domains: Photosystem I PsaF, reaction centre subunit III
Photosystem I reaction center subunit V, chloroplastic Chain: G
Molecule details ›
Chain: G
Length: 97 amino acids
Theoretical weight: 10.68 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q9S7N7 (Residues: 62-158; Coverage: 61%)
Gene names: At1g55670, F20N2.21, F20N2.33, F20N2_3, PSAG
Sequence domains: Photosystem I psaG / psaK
Photosystem I reaction center subunit VI Chain: H
Molecule details ›
Chain: H
Length: 88 amino acids
Theoretical weight: 9.49 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: A0A0M3KL10 (Residues: 2-87; Coverage: 96%)
Sequence domains: Photosystem I reaction centre subunit VI
Photosystem I reaction center subunit VIII Chain: I
Molecule details ›
Chain: I
Length: 40 amino acids
Theoretical weight: 4.47 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P17227 (Residues: 1-40; Coverage: 100%)
Gene name: psaI
Sequence domains: Photosystem I reaction centre subunit VIII
Photosystem I reaction center subunit IX Chain: J
Molecule details ›
Chain: J
Length: 42 amino acids
Theoretical weight: 4.77 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: D5MAL3 (Residues: 1-42; Coverage: 100%)
Gene name: psaJ
Sequence domains: Photosystem I reaction centre subunit IX / PsaJ
Structure domains: Single helix bin
PSI-K Chain: K
Molecule details ›
Chain: K
Length: 80 amino acids
Theoretical weight: 7.99 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9L3 (Residues: 3-82; Coverage: 95%)
Sequence domains: Photosystem I psaG / psaK
PSI subunit V Chain: L
Molecule details ›
Chain: L
Length: 157 amino acids
Theoretical weight: 16.56 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9L1 (Residues: 4-160; Coverage: 98%)
Sequence domains: Photosystem I reaction centre subunit XI
Structure domains: Photosystem I PsaL, reaction centre subunit XI

Ligands and Environments

14 bound ligands:
Ligand LUT 7 x LUT
Ligand BCR 27 x BCR
Ligand CLA 142 x CLA
Ligand CHL 13 x CHL
Ligand LHG 7 x LHG
Ligand LMG 20 x LMG
Ligand XAT 2 x XAT
Ligand LMT 10 x LMT
Ligand CA 2 x CA
Ligand DGD 5 x DGD
Ligand CL0 1 x CL0
Ligand SF4 3 x SF4
Ligand PQN 2 x PQN
Ligand ZEX 1 x ZEX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 189.611Å b: 200.994Å c: 212.943Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.21 0.232

Quick links

Citations

11 review citations

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

11 mentions without citation

Photosynthetic Light-Harvesting (Antenna) Complexes-Structures and Functions.
Lokstein et al. (2021)
10 more