› 5zf0

X-ray diffraction
4.2Å resolution

X-ray Structure of the Electron Transfer Complex between Ferredoxin and Photosystem I

Released:
DOI: 10.2210/pdb5zf0/pdb
PDB entry 5zf0 coloured by chain, front view.
PDB entry 5zf0 coloured by chain, side view.
PDB entry 5zf0 coloured by chain, top view.
Source organisms:
Primary publication:
X-ray structure of an asymmetrical trimeric ferredoxin-photosystem I complex.
Kubota-Kawai H, Mutoh R, Shinmura K, Sétif P, Nowaczyk MM, Rögner M, Ikegami T, Tanaka H, Kurisu G
Nat Plants 4 218-224 (2018)
PMID: 29610537

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 39-mer (preferred)
PDBe Complex ID:
PDB-CPX-141200 (preferred)
Entry contents:
13 distinct polypeptide molecules
Macromolecules (13 distinct):
Photosystem I P700 chlorophyll a apoprotein A1 Chains: A1, A2, A3, A4, A5, A6
Molecule details ›
Chains: A1, A2, A3, A4, A5, A6
Length: 755 amino acids
Theoretical weight: 83.27 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: P0A405 (Residues: 1-755; Coverage: 100%)
Gene names: psaA, tlr0731
Sequence domains: Photosystem I psaA/psaB protein
Photosystem I P700 chlorophyll a apoprotein A2 Chains: B1, B2, B3, B4, B5, B6
Molecule details ›
Chains: B1, B2, B3, B4, B5, B6
Length: 740 amino acids
Theoretical weight: 82.99 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: P0A407 (Residues: 2-741; Coverage: 100%)
Gene names: psaB, tlr0732
Sequence domains: Photosystem I psaA/psaB protein
Photosystem I iron-sulfur center Chains: C1, C2, C3, C4, C5, C6
Molecule details ›
Chains: C1, C2, C3, C4, C5, C6
Length: 80 amino acids
Theoretical weight: 8.68 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: P0A415 (Residues: 2-81; Coverage: 99%)
Gene names: psaC, tsl1013
Sequence domains: 4Fe-4S dicluster domain
Photosystem I reaction center subunit II Chains: D1, D2, D3, D4, D5, D6
Molecule details ›
Chains: D1, D2, D3, D4, D5, D6
Length: 138 amino acids
Theoretical weight: 15.26 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: P0A420 (Residues: 2-139; Coverage: 99%)
Gene names: psaD, tll1724
Sequence domains: PsaD
Photosystem I reaction center subunit IV Chains: E1, E2, E3, E4, E5, E6
Molecule details ›
Chains: E1, E2, E3, E4, E5, E6
Length: 75 amino acids
Theoretical weight: 8.27 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: P0A423 (Residues: 2-76; Coverage: 99%)
Gene names: psaE, tsl1567
Sequence domains: Photosystem I reaction centre subunit IV / PsaE
Photosystem I reaction center subunit III Chains: F1, F2, F3, F4, F5, F6
Molecule details ›
Chains: F1, F2, F3, F4, F5, F6
Length: 164 amino acids
Theoretical weight: 17.72 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: P0A401 (Residues: 1-164; Coverage: 100%)
Gene names: psaF, tlr2411
Sequence domains: Photosystem I reaction centre subunit III
Photosystem I reaction center subunit VIII Chains: I1, I2, I3, I4, I5, I6
Molecule details ›
Chains: I1, I2, I3, I4, I5, I6
Length: 38 amino acids
Theoretical weight: 4.3 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: P0A427 (Residues: 1-38; Coverage: 100%)
Gene names: psaI, tsr2405
Sequence domains: Photosystem I reaction centre subunit VIII
Photosystem I reaction center subunit IX Chains: J1, J2, J3, J4, J5, J6
Molecule details ›
Chains: J1, J2, J3, J4, J5, J6
Length: 41 amino acids
Theoretical weight: 4.77 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: P0A429 (Residues: 1-41; Coverage: 100%)
Gene names: psaJ, tsr2412
Sequence domains: Photosystem I reaction centre subunit IX / PsaJ
Photosystem I reaction center subunit PsaK Chains: K1, K2, K3, K4, K5, K6
Molecule details ›
Chains: K1, K2, K3, K4, K5, K6
Length: 83 amino acids
Theoretical weight: 8.48 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: P0A425 (Residues: 1-83; Coverage: 100%)
Gene names: psaK, tsr2273
Sequence domains: Photosystem I psaG / psaK
Photosystem I reaction center subunit XI Chains: L1, L2, L3, L4, L5, L6
Molecule details ›
Chains: L1, L2, L3, L4, L5, L6
Length: 154 amino acids
Theoretical weight: 16.16 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: Q8DGB4 (Residues: 2-155; Coverage: 99%)
Gene names: psaL, tlr2404
Sequence domains: Photosystem I reaction centre subunit XI
Photosystem I reaction center subunit XII Chains: M1, M2, M3, M4, M5, M6
Molecule details ›
Chains: M1, M2, M3, M4, M5, M6
Length: 31 amino acids
Theoretical weight: 3.43 KDa
Source organism: Thermosynechococcus vestitus BP-1
UniProt:
  • Canonical: P0A403 (Residues: 1-31; Coverage: 100%)
Gene names: psaM, tsr0197
Sequence domains: Photosystem I protein M (PsaM)
PsaX Chains: X1, X2, X3, X4, X5, X6
Molecule details ›
Chains: X1, X2, X3, X4, X5, X6
Length: 35 amino acids
Theoretical weight: 3.85 KDa
Source organism: Thermosynechococcus vestitus
Ferredoxin-1 Chains: P1, P2, P3, P4, P5, P6
Molecule details ›
Chains: P1, P2, P3, P4, P5, P6
Length: 97 amino acids
Theoretical weight: 10.72 KDa
Source organism: Thermosynechococcus vestitus BP-1
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A3C9 (Residues: 2-98; Coverage: 99%)
Gene names: petF, petF1, tsl1009
Sequence domains: 2Fe-2S iron-sulfur cluster binding domain

Ligands and Environments

8 bound ligands:
Ligand CLA 576 x CLA
Ligand PQN 12 x PQN
Ligand BCR 132 x BCR
Ligand LHG 18 x LHG
Ligand SF4 18 x SF4
Ligand LMG 6 x LMG
Ligand CA 6 x CA
Ligand FES 6 x FES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21
Unit cell:
a: 214.101Å b: 239.668Å c: 265.605Å
α: 90° β: 101.08° γ: 90°
R-values:
R R work R free
0.354 0.353 0.377
Expression system: Escherichia coli

Quick links

Citations

17 citation in other articles

Structure of the complex I-like molecule NDH of oxygenic photosynthesis.
Laughlin et al. (2019)
16 more

7 mentions without citation

Structural insights into NDH-1 mediated cyclic electron transfer.
Zhang et al. (2020)
6 more