› 4l6v

X-ray diffraction
3.8Å resolution

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

Released:
DOI: 10.2210/pdb4l6v/pdb
PDB entry 4l6v coloured by chain, front view.
PDB entry 4l6v coloured by chain, side view.
PDB entry 4l6v coloured by chain, top view.
Source organisms:
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 decamer (preferred)
PDBe Complex ID:
PDB-CPX-146410 (preferred)
Entry contents:
10 distinct polypeptide molecules
Macromolecules (10 distinct):
Photosystem I P700 chlorophyll a apoprotein A1 Chains: 1, A, a
Molecule details ›
Chains: 1, A, a
Length: 751 amino acids
Theoretical weight: 83.04 KDa
Source organism: Synechocystis sp. PCC 6803
Expression system: Synechocystis sp. PCC 6803
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 Chains: 2, B, b
Molecule details ›
Chains: 2, B, 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 Chains: 3, C, c
Molecule details ›
Chains: 3, C, 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 Chains: 4, D, d
Molecule details ›
Chains: 4, D, 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 Chains: 5, E, e
Molecule details ›
Chains: 5, E, 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; Photosystem I reaction center subunit IX Chains: 6, F, f
Molecule details ›
Chains: 6, F, f
Length: 125 amino acids
Theoretical weight: 13.86 KDa
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
Expression system: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: Q55329 (Residues: 1-40; Coverage: 100%)
  • Canonical: P29256 (Residues: 84-165; Coverage: 58%)
Gene names: psaF, psaJ, sll0819, sml0008
Sequence domains:
Structure domains: Photosystem I PsaF, reaction centre subunit III
Photosystem I reaction center subunit XI Chains: 8, L, l
Molecule details ›
Chains: 8, L, l
Length: 157 amino acids
Theoretical weight: 16.63 KDa
Source organism: Synechocystis sp. PCC 6803
Expression system: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: P37277 (Residues: 1-157; Coverage: 100%)
Gene names: psaL, slr1655
Sequence domains: Photosystem I reaction centre subunit XI
Structure domains: Photosystem I PsaL, reaction centre subunit XI
Photosystem I reaction center subunit XII Chains: 7, M, m
Molecule details ›
Chains: 7, M, 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)
Photosystem I reaction center subunit VIII Chains: 9, I, i
Molecule details ›
Chains: 9, I, i
Length: 40 amino acids
Theoretical weight: 4.41 KDa
Source organism: Synechocystis sp. PCC 6803
Expression system: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: Q55330 (Residues: 1-40; Coverage: 100%)
Gene names: psaI, smr0004
Sequence domains: Photosystem I reaction centre subunit VIII
Photosystem I reaction center subunit PsaK 2 Chains: 0, K, k
Molecule details ›
Chains: 0, K, 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

Ligands and Environments

6 bound ligands:
Ligand CLA 273 x CLA
Ligand PQN 6 x PQN
Ligand SF4 9 x SF4
Ligand BCR 57 x BCR
Ligand LHG 9 x LHG
Ligand LMG 3 x LMG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P21
Unit cell:
a: 214.619Å b: 133.68Å c: 219.846Å
α: 90° β: 111.14° γ: 90°
R-values:
R R work R free
0.255 0.253 0.297
Expression system: 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

Molecular dynamics simulation and bioinformatics study on chloroplast stromal ridge complex from rice (Oryza sativa L.).
Zhang et al. (2016)