› 4xk8

X-ray diffraction
2.8Å resolution

Crystal structure of plant photosystem I-LHCI super-complex at 2.8 angstrom resolution

Released:
DOI: 10.2210/pdb4xk8/pdb
PDB entry 4xk8 coloured by chain, front view.
PDB entry 4xk8 coloured by chain, side view.
PDB entry 4xk8 coloured by chain, top view.
Source organism: Pisum sativum
Primary publication:
Photosynthesis. Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex.
Qin X, Suga M, Kuang T, Shen JR
Science 348 989-95 (2015)
PMID: 26023133

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 hexadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107293 (preferred)
Entry contents:
16 distinct polypeptide molecules
Macromolecules (16 distinct):
Photosystem I P700 chlorophyll a apoprotein A1 Chains: A, a
Molecule details ›
Chains: A, a
Length: 742 amino acids
Theoretical weight: 82.41 KDa
Source organism: Pisum sativum
Expression system: Not provided
UniProt:
  • Canonical: P05310 (Residues: 17-758; Coverage: 98%)
Gene names: psaA, psaA1
Sequence domains: Photosystem I psaA/psaB protein
Structure domains: Photosystem I PsaA/PsaB
Photosystem I P700 chlorophyll a apoprotein A2 Chains: B, b
Molecule details ›
Chains: B, b
Length: 733 amino acids
Theoretical weight: 82.47 KDa
Source organism: Pisum sativum
Expression system: Not provided
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 Chains: C, c
Molecule details ›
Chains: C, c
Length: 80 amino acids
Theoretical weight: 8.86 KDa
Source organism: Pisum sativum
Expression system: Not provided
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 Chains: D, d
Molecule details ›
Chains: D, d
Length: 141 amino acids
Theoretical weight: 15.85 KDa
Source organism: Pisum sativum
Expression system: Not provided
UniProt:
  • Canonical: A5Z2K3 (Residues: 70-210; Coverage: 67%)
Gene names: 100101915, GLYMA_10G249000, psaD
Sequence domains: PsaD
Structure domains: Photosystem I PsaD, reaction center subunit II
Photosystem I reaction center subunit IV Chains: E, e
Molecule details ›
Chains: E, e
Length: 64 amino acids
Theoretical weight: 7.3 KDa
Source organism: Pisum sativum
Expression system: Not provided
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 Chains: F, f
Molecule details ›
Chains: F, f
Length: 151 amino acids
Theoretical weight: 17.01 KDa
Source organism: Pisum sativum
Expression system: Not provided
UniProt:
  • Canonical: P12355 (Residues: 78-228; Coverage: 65%)
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, chloroplastic Chains: G, g
Molecule details ›
Chains: G, g
Length: 95 amino acids
Theoretical weight: 10.46 KDa
Source organism: Pisum sativum
Expression system: Not provided
UniProt:
  • Canonical: P12357 (Residues: 70-164; Coverage: 57%)
Gene name: PSAG
Sequence domains: Photosystem I psaG / psaK
Photosystem I reaction center subunit VI Chains: H, h
Molecule details ›
Chains: H, h
Length: 90 amino acids
Theoretical weight: 9.64 KDa
Source organism: Pisum sativum
Expression system: Not provided
UniProt:
  • Canonical: C6T221 (Residues: 50-139; Coverage: 65%)
Sequence domains: Photosystem I reaction centre subunit VI
Photosystem I reaction center subunit VIII Chains: I, i
Molecule details ›
Chains: I, i
Length: 30 amino acids
Theoretical weight: 3.3 KDa
Source organism: Pisum sativum
Expression system: Not provided
UniProt:
  • Canonical: P17227 (Residues: 2-31; Coverage: 75%)
Gene name: psaI
Sequence domains: Photosystem I reaction centre subunit VIII
Photosystem I reaction center subunit IX Chains: J, j
Molecule details ›
Chains: J, j
Length: 39 amino acids
Theoretical weight: 4.4 KDa
Source organism: Pisum sativum
Expression system: Not provided
UniProt:
  • Canonical: A4GGC6 (Residues: 1-39; Coverage: 89%)
Gene name: psaJ
Sequence domains: Photosystem I reaction centre subunit IX / PsaJ
PSI-K Chains: K, k
Molecule details ›
Chains: K, k
Length: 84 amino acids
Theoretical weight: 8.46 KDa
Source organism: Pisum sativum
Expression system: Not provided
UniProt:
  • Canonical: E1C9L3 (Residues: 1-84; Coverage: 100%)
Sequence domains: Photosystem I psaG / psaK
PSI subunit V Chains: L, l
Molecule details ›
Chains: L, l
Length: 153 amino acids
Theoretical weight: 16.13 KDa
Source organism: Pisum sativum
Expression system: Not provided
UniProt:
  • Canonical: E1C9L1 (Residues: 4-156; Coverage: 95%)
Sequence domains: Photosystem I reaction centre subunit XI
Structure domains: Photosystem I PsaL, reaction centre subunit XI
Chlorophyll a-b binding protein 6, chloroplastic Chains: 1, 6
Molecule details ›
Chains: 1, 6
Length: 195 amino acids
Theoretical weight: 21.35 KDa
Source organism: Pisum sativum
Expression system: Not provided
UniProt:
  • Canonical: Q01667 (Residues: 46-240; Coverage: 81%)
Gene names: At3g54890, CAB6, F28P10.130, LHCA1
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chains: 2, 7
Molecule details ›
Chains: 2, 7
Length: 206 amino acids
Theoretical weight: 22.69 KDa
Source organism: Pisum sativum
Expression system: Not provided
UniProt:
  • Canonical: Q41038 (Residues: 62-267; Coverage: 77%)
Gene names: KIW84_045602, lhaB
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein 3, chloroplastic Chains: 3, 8
Molecule details ›
Chains: 3, 8
Length: 218 amino acids
Theoretical weight: 23.73 KDa
Source organism: Pisum sativum
Expression system: Not provided
UniProt:
  • Canonical: Q32904 (Residues: 55-272; Coverage: 79%)
Gene name: lhca3
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein P4, chloroplastic Chains: 4, 9
Molecule details ›
Chains: 4, 9
Length: 196 amino acids
Theoretical weight: 21.72 KDa
Source organism: Pisum sativum
Expression system: Not provided
UniProt:
  • Canonical: Q9SQL2 (Residues: 54-249; Coverage: 78%)
Gene name: lhcA-P4
Sequence domains: Chlorophyll A-B binding protein

Ligands and Environments

12 bound ligands:
Ligand CLA 285 x CLA
Ligand PQN 4 x PQN
Ligand LHG 11 x LHG
Ligand BCR 52 x BCR
Ligand SF4 6 x SF4
Ligand HTG 6 x HTG
Ligand LMT 1 x LMT
Ligand DGD 2 x DGD
Ligand LMG 5 x LMG
Ligand CHL 24 x CHL
Ligand LUT 10 x LUT
Ligand XAT 8 x XAT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21
Unit cell:
a: 165.624Å b: 192.22Å c: 175.089Å
α: 90° β: 91.41° γ: 90°
R-values:
R R work R free
0.212 0.21 0.248
Expression system: Not provided

Quick links

Citations

17 review citations

Role of membrane glycerolipids in photosynthesis, thylakoid biogenesis and chloroplast development.
Kobayashi K. (2016)
16 more

18 mentions without citation

Photosynthesis.
Johnson MP. (2016)
17 more