› 3lw5

X-ray diffraction
3.3Å resolution

Improved model of plant photosystem I

Released:
DOI: 10.2210/pdb3lw5/pdb
PDB entry 3lw5 coloured by chain, front view.
PDB entry 3lw5 coloured by chain, side view.
PDB entry 3lw5 coloured by chain, top view.
Source organisms:
Primary publication:
Structure determination and improved model of plant photosystem I.
Amunts A, Toporik H, Borovikova A, Nelson N
J Biol Chem 285 3478-86 (2010)
PMID: 19923216

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 octadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-122784 (preferred)
Entry contents:
18 distinct polypeptide molecules
Macromolecules (18 distinct):
Photosystem I P700 chlorophyll a apoprotein A1 Chain: A
Molecule details ›
Chain: A
Length: 738 amino acids
Theoretical weight: 82.02 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P05310 (Residues: 21-758; Coverage: 97%)
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: 733 amino acids
Theoretical weight: 82.36 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P05311 (Residues: 2-734; 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: 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: 138 amino acids
Theoretical weight: 15.56 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: 64 amino acids
Theoretical weight: 7.27 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, chloroplastic Chain: F
Molecule details ›
Chain: F
Length: 154 amino acids
Theoretical weight: 17.3 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P12355 (Residues: 78-231; Coverage: 67%)
Gene name: PSAF
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: 95 amino acids
Theoretical weight: 10.46 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P20120 (Residues: 5-39; Coverage: 87%)
Gene name: PSAG
Sequence domains: Photosystem I psaG / psaK
Structure domains: Chlorophyll a-b binding protein like
Photosystem I reaction center subunit VI Chain: H
Molecule details ›
Chain: H
Length: 69 amino acids
Theoretical weight: 7.31 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: 30 amino acids
Theoretical weight: 3.27 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P17227 (Residues: 1-30; Coverage: 75%)
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: 4.79 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9L0 (Residues: 1-42; Coverage: 100%)
Sequence domains: Photosystem I reaction centre subunit IX / PsaJ
Structure domains: Single helix bin
PSI-K Chain: K
Molecule details ›
Chain: K
Length: 84 amino acids
Theoretical weight: 8.46 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9L3 (Residues: 1-84; Coverage: 100%)
Sequence domains: Photosystem I psaG / psaK
Structure domains: Chlorophyll a-b binding protein like
PSI subunit V Chain: L
Molecule details ›
Chain: L
Length: 161 amino acids
Theoretical weight: 17.06 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: 9.77 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)
Structure domains: Chlorophyll A-B binding protein
CHAIN R Chain: R
Molecule details ›
Chain: R
Length: 53 amino acids
Theoretical weight: 4.53 KDa
Source organism: unidentified
Chlorophyll a-b binding protein, chloroplastic Chain: 1
Molecule details ›
Chain: 1
Length: 170 amino acids
Theoretical weight: 18.62 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: 176 amino acids
Theoretical weight: 19.53 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q41038 (Residues: 94-269; Coverage: 65%)
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: 172 amino acids
Theoretical weight: 18.72 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q32904 (Residues: 84-255; Coverage: 63%)
Gene name: lhca3
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein P4, chloroplastic Chain: 4
Molecule details ›
Chain: 4
Length: 166 amino acids
Theoretical weight: 18.7 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q9SQL2 (Residues: 81-247; Coverage: 66%)
Gene name: lhcA-P4
Sequence domains: Chlorophyll A-B binding protein

Ligands and Environments

6 bound ligands:
Ligand CLA 174 x CLA
Ligand PQN 2 x PQN
Ligand BCR 19 x BCR
Ligand LMU 53 x LMU
Ligand SF4 3 x SF4
Ligand LMG 1 x LMG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P21
Unit cell:
a: 120.655Å b: 189.086Å c: 129.388Å
α: 90° β: 91.24° γ: 90°
R-values:
R R work R free
0.351 0.349 0.383

Quick links

Citations

27 review citations

Evolution of photosynthesis.
Hohmann-Marriott et al. (2011)
26 more

4 mentions without citation

Iron sparing and recycling in a compartmentalized cell.
Blaby-Haas et al. (2013)
3 more