› 6ly5

Electron Microscopy
2.38Å resolution

Organization and energy transfer in a huge diatom PSI-FCPI supercomplex

Released:
DOI: 10.2210/pdb6ly5/pdb
PDB entry 6ly5 coloured by chain, front view.
PDB entry 6ly5 coloured by chain, side view.
PDB entry 6ly5 coloured by chain, top view.
Source organism: Chaetoceros gracilis
Primary publication:
Structural basis for energy transfer in a huge diatom PSI-FCPI supercomplex.
Xu C, Pi X, Huang Y, Han G, Chen X, Qin X, Huang G, Zhao S, Yang Y, Kuang T, Wang W, Sui SF, Shen JR
Nat Commun 11 5081 (2020)
PMID: 33033236
Related structures: EMD-30012

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 36-mer (preferred)
PDBe Complex ID:
PDB-CPX-103435 (preferred)
Entry contents:
33 distinct polypeptide molecules
Macromolecules (33 distinct):
Fucoxanthin chlorophyll a/c protein 5 Chain: A
Molecule details ›
Chain: A
Length: 168 amino acids
Theoretical weight: 18.39 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B7P2 (Residues: 38-205; Coverage: 89%)
Gene name: Lhcr5
Sequence domains: Chlorophyll A-B binding protein
Not-an-Elip Chain: B
Molecule details ›
Chain: B
Length: 223 amino acids
Theoretical weight: 24.55 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A1E7F4Y9 (Residues: 1-223; Coverage: 100%)
Gene names: FRACYDRAFT_219042, RedCap
Sequence domains: Chlorophyll A-B binding protein
Fucoxanthin chlorophyll a/c protein 1 Chain: C
Molecule details ›
Chain: C
Length: 198 amino acids
Theoretical weight: 21.11 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B024 (Residues: 1-198; Coverage: 100%)
Gene name: Lhcr1
Sequence domains: Chlorophyll A-B binding protein
Fucoxanthin chlorophyll a/c protein 6 Chain: D
Molecule details ›
Chain: D
Length: 207 amino acids
Theoretical weight: 22.32 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B112 (Residues: 1-208; Coverage: 100%)
Gene name: Lhcr6
Sequence domains: Chlorophyll A-B binding protein
Fucoxanthin chlorophyll a/c protein 7 Chain: E
Molecule details ›
Chain: E
Length: 222 amino acids
Theoretical weight: 23.5 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B3M5 (Residues: 1-222; Coverage: 100%)
Gene name: Lhcr7
Sequence domains: Chlorophyll A-B binding protein
Fucoxanthin chlorophyll a/c protein 4 Chain: F
Molecule details ›
Chain: F
Length: 215 amino acids
Theoretical weight: 23.09 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B492 (Residues: 1-215; Coverage: 100%)
Gene name: Lhcr4
Sequence domains: Chlorophyll A-B binding protein
Fucoxanthin chlorophyll a/c protein 8 Chain: G
Molecule details ›
Chain: G
Length: 245 amino acids
Theoretical weight: 26.61 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B0A4 (Residues: 1-245; Coverage: 100%)
Gene name: Lhcr8
Sequence domains: Chlorophyll A-B binding protein
Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type Chain: H
Molecule details ›
Chain: H
Length: 203 amino acids
Theoretical weight: 21.69 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: B8C0K4 (Residues: 1-203; Coverage: 100%)
Gene names: Lhcr14, THAPSDRAFT_4883
Sequence domains: Chlorophyll A-B binding protein
Fucoxanthin chlorophyll a/c protein 9 Chain: I
Molecule details ›
Chain: I
Length: 195 amino acids
Theoretical weight: 21.18 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B150 (Residues: 1-195; Coverage: 100%)
Gene name: Lhcr9
Sequence domains: Chlorophyll A-B binding protein
Fucoxanthin chlorophyll a/c protein 3 Chain: J
Molecule details ›
Chain: J
Length: 200 amino acids
Theoretical weight: 21.56 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B2D5 (Residues: 1-150; Coverage: 99%)
Gene name: Lhcr3
Sequence domains: Chlorophyll A-B binding protein
Fucoxanthin chlorophyll a/c protein 10 Chain: K
Molecule details ›
Chain: K
Length: 207 amino acids
Theoretical weight: 22.2 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B0S3 (Residues: 1-207; Coverage: 100%)
Gene name: Lhcr10
Sequence domains: Chlorophyll A-B binding protein
Fucoxanthin chlorophyll a/c protein 11 Chain: L
Molecule details ›
Chain: L
Length: 229 amino acids
Theoretical weight: 24.85 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B037 (Residues: 1-229; Coverage: 100%)
Gene name: Lhcq1
Sequence domains: Chlorophyll A-B binding protein
Fucoxanthin chlorophyll a/c protein 13 Chain: M
Molecule details ›
Chain: M
Length: 306 amino acids
Theoretical weight: 32.65 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B2D8 (Residues: 1-244; Coverage: 100%)
Gene name: Lhcq3
Sequence domains: Chlorophyll A-B binding protein
Fucoxanthin chlorophyll a/c protein 15 Chain: N
Molecule details ›
Chain: N
Length: 219 amino acids
Theoretical weight: 24.25 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B7P8 (Residues: 40-258; Coverage: 91%)
Gene name: Lhcq5
Sequence domains: Chlorophyll A-B binding protein
Fucoxanthin chlorophyll a/c protein 16 Chains: O, P, Q
Molecule details ›
Chains: O, P, Q
Length: 205 amino acids
Theoretical weight: 21.82 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B125 (Residues: 1-206; Coverage: 100%)
Gene name: Lhcq6
Sequence domains: Chlorophyll A-B binding protein
Fucoxanthin chlorophyll a/c protein 14 Chain: R
Molecule details ›
Chain: R
Length: 246 amino acids
Theoretical weight: 26.55 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B499 (Residues: 1-249; Coverage: 99%)
Gene name: Lhcq4
Sequence domains: Chlorophyll A-B binding protein
Fucoxanthin chlorophyll a/c protein 15 Chain: S
Molecule details ›
Chain: S
Length: 254 amino acids
Theoretical weight: 27.56 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B7P8 (Residues: 3-261; Coverage: 98%)
Gene name: Lhcq5
Sequence domains: Chlorophyll A-B binding protein
FCPI-12 Chain: T
Molecule details ›
Chain: T
Length: 207 amino acids
Theoretical weight: 22.34 KDa
Source organism: Chaetoceros gracilis
Protein fucoxanthin chlorophyl a/c protein Chains: W, X
Molecule details ›
Chains: W, X
Length: 198 amino acids
Theoretical weight: 21.35 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: B7FRW2 (Residues: 1-198; Coverage: 100%)
Gene names: Lhcf3, Lhcf4, PHATRDRAFT_25168, PHATRDRAFT_50705
Sequence domains: Chlorophyll A-B binding protein
Photosystem I P700 chlorophyll a apoprotein A1 Chain: a
Molecule details ›
Chain: a
Length: 743 amino acids
Theoretical weight: 82.85 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B109 (Residues: 10-752; Coverage: 99%)
Gene name: psaA
Sequence domains: Photosystem I psaA/psaB protein
photosystem I Chain: b
Molecule details ›
Chain: b
Length: 733 amino acids
Theoretical weight: 82.03 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B0E7 (Residues: 1-733; Coverage: 100%)
Gene name: psaB
Sequence domains: Photosystem I psaA/psaB protein
Photosystem I iron-sulfur center Chain: c
Molecule details ›
Chain: c
Length: 80 amino acids
Theoretical weight: 8.86 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: P10793 (Residues: 2-81; Coverage: 99%)
Gene names: frxA, psaC
Sequence domains: 4Fe-4S dicluster domain
Photosystem I reaction center subunit II, chloroplastic Chain: d
Molecule details ›
Chain: d
Length: 132 amino acids
Theoretical weight: 14.94 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A5Z2K3 (Residues: 79-210; Coverage: 63%)
Gene names: 100101915, GLYMA_10G249000, psaD
Sequence domains: PsaD
Photosystem I reaction center subunit IV Chain: e
Molecule details ›
Chain: e
Length: 63 amino acids
Theoretical weight: 7.19 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: E1C9K6 (Residues: 2-64; Coverage: 98%)
Sequence domains: Photosystem I reaction centre subunit IV / PsaE
Photosystem I reaction center subunit III, chloroplastic Chain: f
Molecule details ›
Chain: f
Length: 162 amino acids
Theoretical weight: 17.79 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: P12355 (Residues: 78-228; Coverage: 65%)
Gene name: PSAF
Sequence domains: Photosystem I reaction centre subunit III
Photosystem I reaction center subunit VIII Chain: i
Molecule details ›
Chain: i
Length: 40 amino acids
Theoretical weight: 4.47 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: P17227 (Residues: 1-40; Coverage: 100%)
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: 4.73 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A4GGC6 (Residues: 1-42; Coverage: 96%)
Gene name: psaJ
Sequence domains: Photosystem I reaction centre subunit IX / PsaJ
PSI subunit V Chain: l
Molecule details ›
Chain: l
Length: 172 amino acids
Theoretical weight: 19.03 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B0N3 (Residues: 1-143; Coverage: 95%)
Gene name: psaL
Sequence domains: Photosystem I reaction centre subunit XI
Photosystem I reaction center subunit XII Chain: m
Molecule details ›
Chain: m
Length: 29 amino acids
Theoretical weight: 3.14 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: Q85G73 (Residues: 1-29; Coverage: 100%)
Gene name: psaM
Sequence domains: Photosystem I protein M (PsaM)
PsaS Chain: g
Molecule details ›
Chain: g
Length: 134 amino acids
Theoretical weight: 11.42 KDa
Source organism: Chaetoceros gracilis
Photosystem I reaction center protein 28 Chain: h
Molecule details ›
Chain: h
Length: 139 amino acids
Theoretical weight: 14.77 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: A0A6J4B118 (Residues: 1-139; Coverage: 100%)
Gene name: psa28
FCPI-2 Chain: U
Molecule details ›
Chain: U
Length: 160 amino acids
Theoretical weight: 17.35 KDa
Source organism: Chaetoceros gracilis
FCPI-19 Chain: V
Molecule details ›
Chain: V
Length: 179 amino acids
Theoretical weight: 19.31 KDa
Source organism: Chaetoceros gracilis

Ligands and Environments

12 bound ligands:
Ligand DD6 35 x DD6
Ligand A86 102 x A86
Ligand CLA 326 x CLA
Ligand KC1 34 x KC1
Ligand SQD 2 x SQD
Ligand LMT 26 x LMT
Ligand DGD 3 x DGD
Ligand LHG 22 x LHG
Ligand LMG 16 x LMG
Ligand PQN 2 x PQN
Ligand BCR 18 x BCR
Ligand SF4 3 x SF4
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.38Å
Relevant EMDB volumes: EMD-30012

Quick links

Citations

3 review citations

The Critical Studies of Fucoxanthin Research Trends from 1928 to June 2021: A Bibliometric Review.
Khaw et al. (2021)
2 more

4 mentions without citation

Structural basis for energy transfer in a huge diatom PSI-FCPI supercomplex.
Xu et al. (2020)
3 more