› 8jzf

Electron Microscopy
2.7Å resolution

PSI-AcpPCI supercomplex from Symbiodinium

Released:
DOI: 10.2210/pdb8jzf/pdb
PDB entry 8jzf coloured by chain, front view.
PDB entry 8jzf coloured by chain, side view.
PDB entry 8jzf coloured by chain, top view.
Source organism: Symbiodinium
Primary publication:
Structures and organizations of PSI-AcpPCI supercomplexes from red tidal and coral symbiotic photosynthetic dinoflagellates.
Li X, Li Z, Wang F, Zhao S, Xu C, Mao Z, Duan J, Feng Y, Yang Y, Shen L, Wang G, Yang Y, Yu LJ, Sang M, Han G, Wang X, Kuang T, Shen JR, Wang W
Proc Natl Acad Sci U S A 121 e2315476121 (2024)
PMID: 38319970
Related structures: EMD-36743

Function and Biology Details

Reaction catalysed: 
Reduced plastocyanin + oxidized ferredoxin + light = oxidized plastocyanin + reduced ferredoxin
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 25-mer (preferred)
PDBe Complex ID:
PDB-CPX-268562 (preferred)
Entry contents:
25 distinct polypeptide molecules
Macromolecules (25 distinct):
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-7, acpPCI-7 Chain: I
Molecule details ›
Chain: I
Length: 200 amino acids
Theoretical weight: 21.84 KDa
Source organism: Symbiodinium
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-6, acpPCI-6 Chain: K
Molecule details ›
Chain: K
Length: 177 amino acids
Theoretical weight: 19.6 KDa
Source organism: Symbiodinium
Photosystem I unk Chain: z
Molecule details ›
Chain: z
Length: 78 amino acids
Theoretical weight: 6.66 KDa
Source organism: Symbiodinium
Photosystem I unk Chain: y
Molecule details ›
Chain: y
Length: 131 amino acids
Theoretical weight: 11.17 KDa
Source organism: Symbiodinium
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-8, acpPCI-8 Chain: G
Molecule details ›
Chain: G
Length: 224 amino acids
Theoretical weight: 24.56 KDa
Source organism: Symbiodinium
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-10, acpPCI-10 Chain: A
Molecule details ›
Chain: A
Length: 189 amino acids
Theoretical weight: 20.09 KDa
Source organism: Symbiodinium
Photosystem I iron-sulfur center Chain: c
Molecule details ›
Chain: c
Length: 86 amino acids
Theoretical weight: 9.43 KDa
Source organism: Symbiodinium
UniProt:
  • Canonical: A0A812FX01 (Residues: 84-169; Coverage: 57%)
Gene names: STRI2592_LOCUS156, psaC
Sequence domains: 4Fe-4S dicluster domain
Photosystem I reaction center subunit II Chain: d
Molecule details ›
Chain: d
Length: 218 amino acids
Theoretical weight: 24.88 KDa
Source organism: Symbiodinium
UniProt:
  • Canonical: A0A812HMR4 (Residues: 84-301; Coverage: 78%)
Gene names: STRI2592_LOCUS2026, psaD
Sequence domains: PsaD
Photosystem I reaction center subunit IV Chain: e
Molecule details ›
Chain: e
Length: 73 amino acids
Theoretical weight: 8.27 KDa
Source organism: Symbiodinium
UniProt:
  • Canonical: A0A812XT83 (Residues: 54-126; Coverage: 67%)
Gene names: PSAE, SLIN2456_LOCUS27837
Sequence domains: Photosystem I reaction centre subunit IV / PsaE
Photosystem I reaction center subunit III Chain: f
Molecule details ›
Chain: f
Length: 184 amino acids
Theoretical weight: 20.61 KDa
Source organism: Symbiodinium
UniProt:
  • Canonical: A0A812QHR9 (Residues: 72-255; Coverage: 78%)
Gene names: SLIN2456_LOCUS11972, psaF
Sequence domains: Photosystem I reaction centre subunit III
Photosystem I PsaR Chain: h
Molecule details ›
Chain: h
Length: 131 amino acids
Theoretical weight: 15.22 KDa
Source organism: Symbiodinium
UniProt:
  • Canonical: A0A812Q823 (Residues: 87-217; Coverage: 66%)
Gene name: STRI2592_LOCUS20443
Photosystem I PsaI Chain: i
Molecule details ›
Chain: i
Length: 119 amino acids
Theoretical weight: 13.7 KDa
Source organism: Symbiodinium
UniProt:
  • Canonical: A0A812IJ75 (Residues: 59-177; Coverage: 75%)
Gene name: STRI2592_LOCUS5050
Sequence domains: Photosystem I reaction centre subunit VIII
Photosystem I PsaJ Chain: j
Molecule details ›
Chain: j
Length: 98 amino acids
Theoretical weight: 11.15 KDa
Source organism: Symbiodinium
UniProt:
  • Canonical: A0A812LLR4 (Residues: 474-571; Coverage: 17%)
Gene name: SNAT2548_LOCUS11250
PSI subunit V Chain: l
Molecule details ›
Chain: l
Length: 250 amino acids
Theoretical weight: 27.71 KDa
Source organism: Symbiodinium
UniProt:
  • Canonical: A0A812S6M2 (Residues: 37-286; Coverage: 87%)
Gene names: STRI2592_LOCUS24809, psaL
Sequence domains: Photosystem I reaction centre subunit XI
Photosystem I PsaM Chain: m
Molecule details ›
Chain: m
Length: 79 amino acids
Theoretical weight: 8.53 KDa
Source organism: Symbiodinium
UniProt:
  • Canonical: A0A812M556 (Residues: 65-143; Coverage: 66%)
Gene names: SNAT2548_LOCUS13436, SNAT2548_LOCUS13437, SNAT2548_LOCUS13438
Photosystem I P700 chlorophyll a apoprotein A1 Chain: a
Molecule details ›
Chain: a
Length: 670 amino acids
Theoretical weight: 75.79 KDa
Source organism: Symbiodinium
UniProt:
  • Canonical: A0A0A0N2S9 (Residues: 3-672; Coverage: 100%)
Gene name: psaA
Sequence domains: Photosystem I psaA/psaB protein
photosystem I Chain: b
Molecule details ›
Chain: b
Length: 663 amino acids
Theoretical weight: 74.44 KDa
Source organism: Symbiodinium
UniProt:
  • Canonical: A0A0A0N2P0 (Residues: 35-697; Coverage: 95%)
Gene name: psaB
Sequence domains: Photosystem I psaA/psaB protein
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-11, acpPCI-11 Chain: B
Molecule details ›
Chain: B
Length: 192 amino acids
Theoretical weight: 21.26 KDa
Source organism: Symbiodinium
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-9, acpPCI-9 Chain: D
Molecule details ›
Chain: D
Length: 165 amino acids
Theoretical weight: 17.49 KDa
Source organism: Symbiodinium
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-2, acpPCI-2 Chain: F
Molecule details ›
Chain: F
Length: 176 amino acids
Theoretical weight: 19.34 KDa
Source organism: Symbiodinium
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-12, acpPCI-12 Chain: H
Molecule details ›
Chain: H
Length: 160 amino acids
Theoretical weight: 17.11 KDa
Source organism: Symbiodinium
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-3, acpPCI-3 Chain: J
Molecule details ›
Chain: J
Length: 220 amino acids
Theoretical weight: 22.91 KDa
Source organism: Symbiodinium
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-5, acpPCI-5 Chain: L
Molecule details ›
Chain: L
Length: 185 amino acids
Theoretical weight: 20.59 KDa
Source organism: Symbiodinium
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-4, acpPCI-4 Chain: M
Molecule details ›
Chain: M
Length: 173 amino acids
Theoretical weight: 19.38 KDa
Source organism: Symbiodinium
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-13, acpPCI-13 Chain: N
Molecule details ›
Chain: N
Length: 160 amino acids
Theoretical weight: 17.12 KDa
Source organism: Symbiodinium

Ligands and Environments

12 bound ligands:
Ligand DD6 41 x DD6
Ligand UIX 7 x UIX
Ligand CLA 189 x CLA
Ligand KC1 20 x KC1
Ligand DGD 7 x DGD
Ligand LMG 9 x LMG
Ligand PID 18 x PID
Ligand SQD 1 x SQD
Ligand SF4 3 x SF4
Ligand BCR 12 x BCR
Ligand PQN 2 x PQN
Ligand LHG 1 x LHG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.7Å
Relevant EMDB volumes: EMD-36743

Quick links

Citations

2 review citations

Investigating the Balance between Structural Conservation and Functional Flexibility in Photosystem I.
Nelson N. (2024)
1 more

1 mention without citation

Shining light on dinoflagellate photosystem I.
Lin et al. (2024)