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

Electron Microscopy
2.38Å resolution
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
Assembly composition:
hetero 36-mer (preferred)
Entry contents: 33 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 36-mer
PDBe Complex ID: PDB-CPX-103435

Macromolecules

Fucoxanthin chlorophyll a/c protein 5
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
Pfam: Chlorophyll A-B binding protein
InterPro:
Fucoxanthin chlorophyll a/c protein 5 in PDB entry 6ly5, assembly 1, front view.
Fucoxanthin chlorophyll a/c protein 5 in PDB entry 6ly5, assembly 1, side view.
Fucoxanthin chlorophyll a/c protein 5 in PDB entry 6ly5, assembly 1, top view.
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Not-an-Elip
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
Pfam: Chlorophyll A-B binding protein
InterPro: Chlorophyll A-B binding protein
Not-an-Elip in PDB entry 6ly5, assembly 1, front view.
Not-an-Elip in PDB entry 6ly5, assembly 1, side view.
Not-an-Elip in PDB entry 6ly5, assembly 1, top view.
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Fucoxanthin chlorophyll a/c protein 1
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
Pfam: Chlorophyll A-B binding protein
InterPro:
Fucoxanthin chlorophyll a/c protein 1 in PDB entry 6ly5, assembly 1, front view.
Fucoxanthin chlorophyll a/c protein 1 in PDB entry 6ly5, assembly 1, side view.
Fucoxanthin chlorophyll a/c protein 1 in PDB entry 6ly5, assembly 1, top view.
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Fucoxanthin chlorophyll a/c protein 6
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
Pfam: Chlorophyll A-B binding protein
InterPro:
Fucoxanthin chlorophyll a/c protein 6 in PDB entry 6ly5, assembly 1, front view.
Fucoxanthin chlorophyll a/c protein 6 in PDB entry 6ly5, assembly 1, side view.
Fucoxanthin chlorophyll a/c protein 6 in PDB entry 6ly5, assembly 1, top view.
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Fucoxanthin chlorophyll a/c protein 7
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
Pfam: Chlorophyll A-B binding protein
InterPro:
Fucoxanthin chlorophyll a/c protein 7 in PDB entry 6ly5, assembly 1, front view.
Fucoxanthin chlorophyll a/c protein 7 in PDB entry 6ly5, assembly 1, side view.
Fucoxanthin chlorophyll a/c protein 7 in PDB entry 6ly5, assembly 1, top view.
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Fucoxanthin chlorophyll a/c protein 4
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
Pfam: Chlorophyll A-B binding protein
InterPro:
Fucoxanthin chlorophyll a/c protein 4 in PDB entry 6ly5, assembly 1, front view.
Fucoxanthin chlorophyll a/c protein 4 in PDB entry 6ly5, assembly 1, side view.
Fucoxanthin chlorophyll a/c protein 4 in PDB entry 6ly5, assembly 1, top view.
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Fucoxanthin chlorophyll a/c protein 8
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
Pfam: Chlorophyll A-B binding protein
InterPro:
Fucoxanthin chlorophyll a/c protein 8 in PDB entry 6ly5, assembly 1, front view.
Fucoxanthin chlorophyll a/c protein 8 in PDB entry 6ly5, assembly 1, side view.
Fucoxanthin chlorophyll a/c protein 8 in PDB entry 6ly5, assembly 1, top view.
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Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type
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
Pfam: Chlorophyll A-B binding protein
InterPro:
Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type in PDB entry 6ly5, assembly 1, front view.
Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type in PDB entry 6ly5, assembly 1, side view.
Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type in PDB entry 6ly5, assembly 1, top view.
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Fucoxanthin chlorophyll a/c protein 9
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
Pfam: Chlorophyll A-B binding protein
InterPro:
Fucoxanthin chlorophyll a/c protein 9 in PDB entry 6ly5, assembly 1, front view.
Fucoxanthin chlorophyll a/c protein 9 in PDB entry 6ly5, assembly 1, side view.
Fucoxanthin chlorophyll a/c protein 9 in PDB entry 6ly5, assembly 1, top view.
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Fucoxanthin chlorophyll a/c protein 3
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
Pfam: Chlorophyll A-B binding protein
InterPro:
Fucoxanthin chlorophyll a/c protein 3 in PDB entry 6ly5, assembly 1, front view.
Fucoxanthin chlorophyll a/c protein 3 in PDB entry 6ly5, assembly 1, side view.
Fucoxanthin chlorophyll a/c protein 3 in PDB entry 6ly5, assembly 1, top view.
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Fucoxanthin chlorophyll a/c protein 10
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
Pfam: Chlorophyll A-B binding protein
InterPro:
Fucoxanthin chlorophyll a/c protein 10 in PDB entry 6ly5, assembly 1, front view.
Fucoxanthin chlorophyll a/c protein 10 in PDB entry 6ly5, assembly 1, side view.
Fucoxanthin chlorophyll a/c protein 10 in PDB entry 6ly5, assembly 1, top view.
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Fucoxanthin chlorophyll a/c protein 11
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
Pfam: Chlorophyll A-B binding protein
InterPro:
Fucoxanthin chlorophyll a/c protein 11 in PDB entry 6ly5, assembly 1, front view.
Fucoxanthin chlorophyll a/c protein 11 in PDB entry 6ly5, assembly 1, side view.
Fucoxanthin chlorophyll a/c protein 11 in PDB entry 6ly5, assembly 1, top view.
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Fucoxanthin chlorophyll a/c protein 13
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
Pfam: Chlorophyll A-B binding protein
InterPro:
Fucoxanthin chlorophyll a/c protein 13 in PDB entry 6ly5, assembly 1, front view.
Fucoxanthin chlorophyll a/c protein 13 in PDB entry 6ly5, assembly 1, side view.
Fucoxanthin chlorophyll a/c protein 13 in PDB entry 6ly5, assembly 1, top view.
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Fucoxanthin chlorophyll a/c protein 15
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
Pfam: Chlorophyll A-B binding protein
InterPro:
Fucoxanthin chlorophyll a/c protein 15 in PDB entry 6ly5, assembly 1, front view.
Fucoxanthin chlorophyll a/c protein 15 in PDB entry 6ly5, assembly 1, side view.
Fucoxanthin chlorophyll a/c protein 15 in PDB entry 6ly5, assembly 1, top view.
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Fucoxanthin chlorophyll a/c protein 16
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
Pfam: Chlorophyll A-B binding protein
InterPro:
Fucoxanthin chlorophyll a/c protein 16 in PDB entry 6ly5, assembly 1, front view.
Fucoxanthin chlorophyll a/c protein 16 in PDB entry 6ly5, assembly 1, side view.
Fucoxanthin chlorophyll a/c protein 16 in PDB entry 6ly5, assembly 1, top view.
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Fucoxanthin chlorophyll a/c protein 14
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
Pfam: Chlorophyll A-B binding protein
InterPro:
Fucoxanthin chlorophyll a/c protein 14 in PDB entry 6ly5, assembly 1, front view.
Fucoxanthin chlorophyll a/c protein 14 in PDB entry 6ly5, assembly 1, side view.
Fucoxanthin chlorophyll a/c protein 14 in PDB entry 6ly5, assembly 1, top view.
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Fucoxanthin chlorophyll a/c protein 15
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
Pfam: Chlorophyll A-B binding protein
InterPro:
Fucoxanthin chlorophyll a/c protein 15 in PDB entry 6ly5, assembly 1, front view.
Fucoxanthin chlorophyll a/c protein 15 in PDB entry 6ly5, assembly 1, side view.
Fucoxanthin chlorophyll a/c protein 15 in PDB entry 6ly5, assembly 1, top view.
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FCPI-12
Chain: T
Length: 207 amino acids
Theoretical weight: 22.34 KDa
Source organism: Chaetoceros gracilis
InterPro:
FCPI-12 in PDB entry 6ly5, assembly 1, front view.
FCPI-12 in PDB entry 6ly5, assembly 1, side view.
FCPI-12 in PDB entry 6ly5, assembly 1, top view.
Molecule details ›

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Protein fucoxanthin chlorophyl a/c protein
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
Pfam: Chlorophyll A-B binding protein
InterPro:
Protein fucoxanthin chlorophyll a/c protein in PDB entry 6ly5, assembly 1, front view.
Protein fucoxanthin chlorophyll a/c protein in PDB entry 6ly5, assembly 1, side view.
Protein fucoxanthin chlorophyll a/c protein in PDB entry 6ly5, assembly 1, top view.
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Photosystem I P700 chlorophyll a apoprotein A1
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
Pfam: Photosystem I psaA/psaB protein
InterPro:
Photosystem I P700 chlorophyll a apoprotein A1 in PDB entry 6ly5, assembly 1, front view.
Photosystem I P700 chlorophyll a apoprotein A1 in PDB entry 6ly5, assembly 1, side view.
Photosystem I P700 chlorophyll a apoprotein A1 in PDB entry 6ly5, assembly 1, top view.
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photosystem I
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
Pfam: Photosystem I psaA/psaB protein
InterPro:
photosystem I in PDB entry 6ly5, assembly 1, front view.
photosystem I in PDB entry 6ly5, assembly 1, side view.
photosystem I in PDB entry 6ly5, assembly 1, top view.
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Photosystem I iron-sulfur center
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
Pfam: 4Fe-4S dicluster domain
InterPro:
Photosystem I iron-sulfur center in PDB entry 6ly5, assembly 1, front view.
Photosystem I iron-sulfur center in PDB entry 6ly5, assembly 1, side view.
Photosystem I iron-sulfur center in PDB entry 6ly5, assembly 1, top view.
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Photosystem I reaction center subunit II, chloroplastic
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
Pfam: PsaD
InterPro:
Photosystem I reaction center subunit II, chloroplastic in PDB entry 6ly5, assembly 1, front view.
Photosystem I reaction center subunit II, chloroplastic in PDB entry 6ly5, assembly 1, side view.
Photosystem I reaction center subunit II, chloroplastic in PDB entry 6ly5, assembly 1, top view.
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Photosystem I reaction center subunit IV
Chain: e
Length: 63 amino acids
Theoretical weight: 7.19 KDa
Source organism: Chaetoceros gracilis
UniProt:
  • Canonical: E1C9K6 (Residues: 2-64; Coverage: 98%)
Pfam: Photosystem I reaction centre subunit IV / PsaE
InterPro:
Photosystem I reaction center subunit IV in PDB entry 6ly5, assembly 1, front view.
Photosystem I reaction center subunit IV in PDB entry 6ly5, assembly 1, side view.
Photosystem I reaction center subunit IV in PDB entry 6ly5, assembly 1, top view.
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Photosystem I reaction center subunit III, chloroplastic
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
Pfam: Photosystem I reaction centre subunit III
InterPro:
Photosystem I reaction center subunit III, chloroplastic in PDB entry 6ly5, assembly 1, front view.
Photosystem I reaction center subunit III, chloroplastic in PDB entry 6ly5, assembly 1, side view.
Photosystem I reaction center subunit III, chloroplastic in PDB entry 6ly5, assembly 1, top view.
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Photosystem I reaction center subunit VIII
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
Pfam: Photosystem I reaction centre subunit VIII
InterPro:
Photosystem I reaction center subunit VIII in PDB entry 6ly5, assembly 1, front view.
Photosystem I reaction center subunit VIII in PDB entry 6ly5, assembly 1, side view.
Photosystem I reaction center subunit VIII in PDB entry 6ly5, assembly 1, top view.
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Photosystem I reaction center subunit IX
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
Pfam: Photosystem I reaction centre subunit IX / PsaJ
InterPro:
Photosystem I reaction center subunit IX in PDB entry 6ly5, assembly 1, front view.
Photosystem I reaction center subunit IX in PDB entry 6ly5, assembly 1, side view.
Photosystem I reaction center subunit IX in PDB entry 6ly5, assembly 1, top view.
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PSI subunit V
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
Pfam: Photosystem I reaction centre subunit XI
InterPro:
PSI subunit V in PDB entry 6ly5, assembly 1, front view.
PSI subunit V in PDB entry 6ly5, assembly 1, side view.
PSI subunit V in PDB entry 6ly5, assembly 1, top view.
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Photosystem I reaction center subunit XII
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
Pfam: Photosystem I protein M (PsaM)
InterPro:
Photosystem I reaction center subunit XII in PDB entry 6ly5, assembly 1, front view.
Photosystem I reaction center subunit XII in PDB entry 6ly5, assembly 1, side view.
Photosystem I reaction center subunit XII in PDB entry 6ly5, assembly 1, top view.
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PsaS
Chain: g
Length: 134 amino acids
Theoretical weight: 11.42 KDa
Source organism: Chaetoceros gracilis
PsaS in PDB entry 6ly5, assembly 1, front view.
PsaS in PDB entry 6ly5, assembly 1, side view.
PsaS in PDB entry 6ly5, assembly 1, top view.
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Photosystem I reaction center protein 28
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
Photosystem I reaction center protein 28 in PDB entry 6ly5, assembly 1, front view.
Photosystem I reaction center protein 28 in PDB entry 6ly5, assembly 1, side view.
Photosystem I reaction center protein 28 in PDB entry 6ly5, assembly 1, top view.
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FCPI-2
Chain: U
Length: 160 amino acids
Theoretical weight: 17.35 KDa
Source organism: Chaetoceros gracilis
InterPro:
FCPI-2 in PDB entry 6ly5, assembly 1, front view.
FCPI-2 in PDB entry 6ly5, assembly 1, side view.
FCPI-2 in PDB entry 6ly5, assembly 1, top view.
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FCPI-19
Chain: V
Length: 179 amino acids
Theoretical weight: 19.31 KDa
Source organism: Chaetoceros gracilis
InterPro:
FCPI-19 in PDB entry 6ly5, assembly 1, front view.
FCPI-19 in PDB entry 6ly5, assembly 1, side view.
FCPI-19 in PDB entry 6ly5, assembly 1, top view.
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