› 4rku

X-ray diffraction
3Å resolution

Crystal structure of plant Photosystem I at 3 Angstrom resolution

Released:
DOI: 10.2210/pdb4rku/pdb
PDB entry 4rku coloured by chain, front view.
PDB entry 4rku coloured by chain, side view.
PDB entry 4rku coloured by chain, top view.
Source organism: Pisum sativum
Entry authors: Mazor Y, Borovikova A, Greenberg I, Nelson N

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 heptadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-101377 (preferred)
Entry contents:
17 distinct polypeptide molecules
Macromolecules (17 distinct):
Photosystem I P700 chlorophyll a apoprotein A1 Chain: A
Molecule details ›
Chain: A
Length: 721 amino acids
Theoretical weight: 80.08 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P05310 (Residues: 38-758; Coverage: 95%)
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: 731 amino acids
Theoretical weight: 82.28 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P05311 (Residues: 3-733; Coverage: 100%)
Gene names: psaA2, 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: 80 amino acids
Theoretical weight: 8.86 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P10793 (Residues: 2-81; Coverage: 99%)
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: 137 amino acids
Theoretical weight: 15.35 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9K8 (Residues: 1-134; Coverage: 97%)
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: 63 amino acids
Theoretical weight: 7.18 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9K6 (Residues: 1-62; Coverage: 97%)
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: 152 amino acids
Theoretical weight: 17.03 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: A0A0H2UKZ4 (Residues: 1-152; 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 Chain: G
Molecule details ›
Chain: G
Length: 84 amino acids
Theoretical weight: 9.08 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P20120 (Residues: 4-39; Coverage: 90%)
Gene name: PSAG
Sequence domains: Photosystem I psaG / psaK
Photosystem I reaction center subunit VI Chain: H
Molecule details ›
Chain: H
Length: 82 amino acids
Theoretical weight: 8.9 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9K9 (Residues: 1-69; Coverage: 100%)
Sequence domains: Photosystem I reaction centre subunit VI
Photosystem I reaction center subunit VIII Chain: I
Molecule details ›
Chain: I
Length: 26 amino acids
Theoretical weight: 2.8 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P17227 (Residues: 5-30; Coverage: 65%)
Gene name: psaI
Sequence domains: Photosystem I reaction centre subunit VIII
Photosystem I reaction center subunit IX Chain: J
Molecule details ›
Chain: J
Length: 40 amino acids
Theoretical weight: 4.46 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: D5MAL3 (Residues: 2-41; Coverage: 95%)
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: 72 amino acids
Theoretical weight: 7.26 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9L3 (Residues: 1-72; Coverage: 86%)
Sequence domains: Photosystem I psaG / psaK
PSI subunit V Chain: L
Molecule details ›
Chain: L
Length: 163 amino acids
Theoretical weight: 17.31 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9L1 (Residues: 1-161; Coverage: 100%)
Sequence domains: Photosystem I reaction centre subunit XI
Structure domains: Photosystem I PsaL, reaction centre subunit XI
Photosystem I-N subunit Chain: N
Molecule details ›
Chain: N
Length: 85 amino acids
Theoretical weight: 9.74 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9K7 (Residues: 1-85; Coverage: 100%)
Sequence domains: Photosystem I reaction centre subunit N (PSAN or PSI-N)
Chlorophyll a-b binding protein, chloroplastic Chain: 1
Molecule details ›
Chain: 1
Length: 182 amino acids
Theoretical weight: 20.1 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: 199 amino acids
Theoretical weight: 21.97 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q41038 (Residues: 59-257; Coverage: 74%)
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: 196 amino acids
Theoretical weight: 21.78 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q9SQL2 (Residues: 53-248; Coverage: 78%)
Gene name: lhcA-P4
Sequence domains: Chlorophyll A-B binding protein

Ligands and Environments

11 bound ligands:
Ligand PQN 2 x PQN
Ligand BCR 21 x BCR
Ligand LHG 5 x LHG
Ligand CLA 157 x CLA
Ligand SF4 3 x SF4
Ligand CL0 1 x CL0
Ligand DGD 1 x DGD
Ligand LMG 2 x LMG
Ligand LUT 6 x LUT
Ligand NEX 1 x NEX
Ligand G3P 1 x G3P
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P21
Unit cell:
a: 120.631Å b: 189.168Å c: 129.667Å
α: 90° β: 91.11° γ: 90°
R-values:
R R work R free
0.259 0.258 0.293

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