› 8jjr

Electron Microscopy
2.8Å resolution

Cryo-EM structure of Symbiodinium photosystem I

Released:
DOI: 10.2210/pdb8jjr/pdb
PDB entry 8jjr coloured by chain, front view.
PDB entry 8jjr coloured by chain, side view.
PDB entry 8jjr coloured by chain, top view.
Source organism: Symbiodinium sp.
Primary publication:
Architecture of symbiotic dinoflagellate photosystem I-light-harvesting supercomplex in Symbiodinium.
Zhao LS, Wang N, Li K, Li CY, Guo JP, He FY, Liu GM, Chen XL, Gao J, Liu LN, Zhang YZ
OpenAccess logo Nat Commun 15 2392 (2024)
PMID: 38493166
Related structures: EMD-36366

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero 26-mer (preferred)
PDBe Complex ID:
PDB-CPX-246214 (preferred)
Entry contents:
26 distinct polypeptide molecules
Macromolecules (26 distinct):
Chlorophyll a-b binding protein, chloroplastic Chain: A
Molecule details ›
Chain: A
Length: 256 amino acids
Theoretical weight: 27.13 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36I308 (Residues: 461-716; Coverage: 36%)
Gene name: EVOR1521_LOCUS7497
Kinesin motor domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 269 amino acids
Theoretical weight: 28.18 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36MZ23 (Residues: 1616-1884; Coverage: 13%)
Gene name: EVOR1521_LOCUS12392
Kinesin motor domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 193 amino acids
Theoretical weight: 21.71 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36MZ23 (Residues: 1887-2079; Coverage: 9%)
Gene name: EVOR1521_LOCUS12392
Chlorophyll a-b binding protein, chloroplastic Chain: D
Molecule details ›
Chain: D
Length: 177 amino acids
Theoretical weight: 19.57 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36JNS8 (Residues: 306-482; Coverage: 25%)
Gene name: EVOR1521_LOCUS30670
PCPI-5 Chain: E
Molecule details ›
Chain: E
Length: 253 amino acids
Theoretical weight: 26.75 KDa
Source organism: Symbiodinium sp.
Rieske domain-containing protein Chain: F
Molecule details ›
Chain: F
Length: 286 amino acids
Theoretical weight: 30.54 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36INW6 (Residues: 1-286; Coverage: 60%)
Gene name: EVOR1521_LOCUS15458
PCPI-4 Chain: G
Molecule details ›
Chain: G
Length: 228 amino acids
Theoretical weight: 24.45 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36I3A4 (Residues: 60-287; Coverage: 49%)
Gene name: EVOR1521_LOCUS8256
Chlorophyll a-b binding protein, chloroplastic Chain: H
Molecule details ›
Chain: H
Length: 271 amino acids
Theoretical weight: 28 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36NGX7 (Residues: 1-271; Coverage: 50%)
Gene name: EVOR1521_LOCUS25779
Chlorophyll a-b binding protein, chloroplastic Chain: I
Molecule details ›
Chain: I
Length: 246 amino acids
Theoretical weight: 27.41 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36HTH0 (Residues: 417-662; Coverage: 38%)
Gene name: EVOR1521_LOCUS3802
PCPI-9 Chain: J
Molecule details ›
Chain: J
Length: 203 amino acids
Theoretical weight: 22.09 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36N2P9 (Residues: 243-445; Coverage: 24%)
Gene name: EVOR1521_LOCUS20619
PCPI-13 Chain: K
Molecule details ›
Chain: K
Length: 226 amino acids
Theoretical weight: 23.29 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36J0D5 (Residues: 12-237; Coverage: 53%)
Gene names: EVOR1521_LOCUS20445, EVOR1521_LOCUS20447, EVOR1521_LOCUS20448
Chlorophyll a-b binding protein, chloroplastic Chain: T
Molecule details ›
Chain: T
Length: 206 amino acids
Theoretical weight: 21.88 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36NBE3 (Residues: 93-298; Coverage: 69%)
Gene name: EVOR1521_LOCUS20446
Chlorophyll a-b binding protein, chloroplastic Chain: U
Molecule details ›
Chain: U
Length: 137 amino acids
Theoretical weight: 15.4 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36JI10 (Residues: 104-238; Coverage: 31%)
Gene name: EVOR1521_LOCUS27602
PsaA Chain: a
Molecule details ›
Chain: a
Length: 687 amino acids
Theoretical weight: 76.58 KDa
Source organism: Symbiodinium sp.
PsaB Chain: b
Molecule details ›
Chain: b
Length: 669 amino acids
Theoretical weight: 74.86 KDa
Source organism: Symbiodinium sp.
PsaC Chain: c
Molecule details ›
Chain: c
Length: 161 amino acids
Theoretical weight: 16.73 KDa
Source organism: Symbiodinium sp.
PsaD Chain: d
Molecule details ›
Chain: d
Length: 295 amino acids
Theoretical weight: 32.75 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36MQP1 (Residues: 538-832; Coverage: 36%)
Gene name: EVOR1521_LOCUS5571
DNA2/NAM7 helicase helicase domain-containing protein Chain: e
Molecule details ›
Chain: e
Length: 121 amino acids
Theoretical weight: 13.09 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36HPY7 (Residues: 603-714; Coverage: 16%)
Gene name: EVOR1521_LOCUS2592
Photosystem I reaction center subunit III Chain: f
Molecule details ›
Chain: f
Length: 279 amino acids
Theoretical weight: 29.73 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36N3P6 (Residues: 1-279; Coverage: 100%)
Gene names: EVOR1521_LOCUS21494, EVOR1521_LOCUS21495, EVOR1521_LOCUS21496
Photosystem I reaction center subunit VIII Chain: i
Molecule details ›
Chain: i
Length: 179 amino acids
Theoretical weight: 19.73 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36J2Y9 (Residues: 35-214; Coverage: 84%)
Gene name: EVOR1521_LOCUS22019
Photosystem I reaction center subunit IX Chain: j
Molecule details ›
Chain: j
Length: 141 amino acids
Theoretical weight: 15.83 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36N211 (Residues: 1-141; Coverage: 100%)
Gene name: EVOR1521_LOCUS14932
PSI subunit V Chain: l
Molecule details ›
Chain: l
Length: 361 amino acids
Theoretical weight: 38.71 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36N262 (Residues: 1-361; Coverage: 100%)
Gene name: EVOR1521_LOCUS13104
PsaM Chain: m
Molecule details ›
Chain: m
Length: 142 amino acids
Theoretical weight: 14.97 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36N6D6 (Residues: 1-142; Coverage: 100%)
Gene names: EVOR1521_LOCUS18897, EVOR1521_LOCUS18898
RNase III domain-containing protein Chain: r
Molecule details ›
Chain: r
Length: 152 amino acids
Theoretical weight: 17.25 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36JF81 (Residues: 404-555; Coverage: 27%)
Gene name: EVOR1521_LOCUS27412
PsaT Chain: x
Molecule details ›
Chain: x
Length: 121 amino acids
Theoretical weight: 13.4 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36INE2 (Residues: 1-121; Coverage: 100%)
Gene names: EVOR1521_LOCUS16170, EVOR1521_LOCUS16171
PsaU Chain: y
Molecule details ›
Chain: y
Length: 223 amino acids
Theoretical weight: 24.3 KDa
Source organism: Symbiodinium sp.
UniProt:
  • Canonical: A0AA36N4B2 (Residues: 1-223; Coverage: 100%)
Gene name: EVOR1521_LOCUS18633

Ligands and Environments

13 bound ligands:
Ligand CLA 196 x CLA
Ligand KC2 20 x KC2
Ligand UIX 16 x UIX
Ligand DD6 41 x DD6
Ligand SQD 3 x SQD
Ligand PID 10 x PID
Ligand LMG 7 x LMG
Ligand LHG 7 x LHG
Ligand DGD 4 x DGD
Ligand LMU 1 x LMU
Ligand PQN 2 x PQN
Ligand BCR 13 x BCR
Ligand SF4 3 x SF4
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.8Å
Relevant EMDB volumes: EMD-36366

Quick links

Citations

2 citation in other articles

Architecture of symbiotic dinoflagellate photosystem I-light-harvesting supercomplex in Symbiodinium.
Zhao et al. (2024)
1 more