› 4kt0

X-ray diffraction
2.8Å resolution

Crystal structure of a virus like photosystem I from the cyanobacterium Synechocystis PCC 6803

Released:
DOI: 10.2210/pdb4kt0/pdb
PDB entry 4kt0 coloured by chain, front view.
PDB entry 4kt0 coloured by chain, side view.
PDB entry 4kt0 coloured by chain, top view.
Source organism: Synechocystis sp. PCC 6803
Primary publication:
Crystal structures of virus-like photosystem I complexes from the mesophilic cyanobacterium Synechocystis PCC 6803.
Mazor Y, Nataf D, Toporik H, Nelson N
Elife 3 e01496 (2013)
PMID: 24473073

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 nonamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146412 (preferred)
Entry contents:
9 distinct polypeptide molecules
Macromolecules (9 distinct):
Photosystem I P700 chlorophyll a apoprotein A1 Chain: A
Molecule details ›
Chain: A
Length: 751 amino acids
Theoretical weight: 83.04 KDa
Source organism: Synechocystis sp. PCC 6803
Expression system: Not provided
UniProt:
  • Canonical: P29254 (Residues: 1-751; Coverage: 100%)
Gene names: psaA, slr1834
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: 81.37 KDa
Source organism: Synechocystis sp. PCC 6803
Expression system: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: P29255 (Residues: 1-731; Coverage: 100%)
Gene names: psaB, slr1835
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: 8.84 KDa
Source organism: Synechocystis sp. PCC 6803
Expression system: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: P32422 (Residues: 1-81; Coverage: 100%)
Gene names: psaC, ssl0563
Sequence domains: 4Fe-4S dicluster domain
Structure domains: Alpha-Beta Plaits
Photosystem I reaction center subunit II Chain: D
Molecule details ›
Chain: D
Length: 141 amino acids
Theoretical weight: 15.66 KDa
Source organism: Synechocystis sp. PCC 6803
Expression system: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: P19569 (Residues: 1-141; Coverage: 100%)
Gene names: psaD, slr0737
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: 74 amino acids
Theoretical weight: 8.15 KDa
Source organism: Synechocystis sp. PCC 6803
Expression system: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: P12975 (Residues: 1-74; Coverage: 100%)
Gene names: psaE, ssr2831
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: 165 amino acids
Theoretical weight: 18.27 KDa
Source organism: Synechocystis sp. PCC 6803
Expression system: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: P29256 (Residues: 1-165; Coverage: 100%)
Gene names: psaF, sll0819
Sequence domains: Photosystem I reaction centre subunit III
Structure domains: Photosystem I PsaF, reaction centre subunit III
Photosystem I reaction center subunit IX Chain: J
Molecule details ›
Chain: J
Length: 40 amino acids
Theoretical weight: 4.54 KDa
Source organism: Synechocystis sp. PCC 6803
Expression system: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: Q55329 (Residues: 1-40; Coverage: 100%)
Gene names: psaJ, sml0008
Sequence domains: Photosystem I reaction centre subunit IX / PsaJ
Structure domains: Single helix bin
Photosystem I reaction center subunit PsaK 2 Chain: K
Molecule details ›
Chain: K
Length: 128 amino acids
Theoretical weight: 13.73 KDa
Source organism: Synechocystis sp. PCC 6803
Expression system: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: P74564 (Residues: 1-90; Coverage: 100%)
Gene names: psaK2, sll0629
Sequence domains: Photosystem I psaG / psaK
Structure domains: Photosystem I PsaK, reaction centre
Photosystem I reaction center subunit XII Chain: M
Molecule details ›
Chain: M
Length: 31 amino acids
Theoretical weight: 3.38 KDa
Source organism: Synechocystis sp. PCC 6803
Expression system: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: P72986 (Residues: 1-31; Coverage: 100%)
Gene names: psaM, smr0005
Sequence domains: Photosystem I protein M (PsaM)

Ligands and Environments

9 bound ligands:
Ligand PQN 2 x PQN
Ligand SF4 3 x SF4
Ligand LHG 4 x LHG
Ligand CL0 2 x CL0
Ligand BCR 17 x BCR
Ligand CLA 90 x CLA
Ligand LMU 2 x LMU
Ligand LMG 1 x LMG
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P212121
Unit cell:
a: 120.179Å b: 173.308Å c: 179.136Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.245
Expression systems:
  • Not provided
  • Synechocystis sp. PCC 6803

Quick links

Citations

5 review citations

Structure and energy transfer in photosystems of oxygenic photosynthesis.
Nelson et al. (2015)
4 more

1 mention without citation

Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers.
Campbell et al. (2019)