› 5zgh

Electron Microscopy
3.82Å resolution

Cryo-EM structure of the red algal PSI-LHCR

Released:
DOI: 10.2210/pdb5zgh/pdb
PDB entry 5zgh coloured by chain, front view.
PDB entry 5zgh coloured by chain, side view.
PDB entry 5zgh coloured by chain, top view.
Source organism: Cyanidioschyzon merolae strain 10D
Primary publication:
Unique organization of photosystem I-light-harvesting supercomplex revealed by cryo-EM from a red alga.
Pi X, Tian L, Dai HE, Qin X, Cheng L, Kuang T, Sui SF, Shen JR
Proc Natl Acad Sci U S A 115 4423-4428 (2018)
PMID: 29632169
Related structures: EMD-6930

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 pentadecamer (preferred)
PDBe Complex ID:
PDB-CPX-125953 (preferred)
Entry contents:
15 distinct polypeptide molecules
Macromolecules (15 distinct):
Similar to light harvesting protein Chain: 1
Molecule details ›
Chain: 1
Length: 175 amino acids
Theoretical weight: 19.81 KDa
Source organism: Cyanidioschyzon merolae strain 10D
UniProt:
  • Canonical: M1VKK5 (Residues: 40-214; Coverage: 82%)
Gene name: CYME_CMQ142C
Sequence domains: Chlorophyll A-B binding protein
Similar to chlorophyll a/b-binding protein, CP24 Chain: 2
Molecule details ›
Chain: 2
Length: 199 amino acids
Theoretical weight: 21.96 KDa
Source organism: Cyanidioschyzon merolae strain 10D
UniProt:
  • Canonical: M1UU36 (Residues: 24-222; Coverage: 90%)
Gene name: CYME_CMN234C
Sequence domains: Chlorophyll A-B binding protein
Lhcr3 Chain: 3
Molecule details ›
Chain: 3
Length: 188 amino acids
Theoretical weight: 20.46 KDa
Source organism: Cyanidioschyzon merolae strain 10D
Photosystem I P700 chlorophyll a apoprotein A1 Chain: A
Molecule details ›
Chain: A
Length: 748 amino acids
Theoretical weight: 82.76 KDa
Source organism: Cyanidioschyzon merolae strain 10D
UniProt:
  • Canonical: Q85FY7 (Residues: 1-748; Coverage: 100%)
Gene name: psaA
Sequence domains: Photosystem I psaA/psaB protein
Photosystem I P700 chlorophyll a apoprotein A2 Chain: B
Molecule details ›
Chain: B
Length: 732 amino acids
Theoretical weight: 82.11 KDa
Source organism: Cyanidioschyzon merolae strain 10D
UniProt:
  • Canonical: Q85FY6 (Residues: 1-732; Coverage: 100%)
Gene name: psaB
Sequence domains: Photosystem I psaA/psaB protein
Photosystem I iron-sulfur center Chain: C
Molecule details ›
Chain: C
Length: 81 amino acids
Theoretical weight: 8.82 KDa
Source organism: Cyanidioschyzon merolae strain 10D
UniProt:
  • Canonical: Q85G47 (Residues: 1-81; Coverage: 100%)
Gene name: psaC
Sequence domains: 4Fe-4S dicluster domain
Structure domains: Alpha-Beta Plaits
Photosystem I reaction center subunit II Chain: D
Molecule details ›
Chain: D
Length: 139 amino acids
Theoretical weight: 15.7 KDa
Source organism: Cyanidioschyzon merolae strain 10D
UniProt:
  • Canonical: Q85FY0 (Residues: 1-139; Coverage: 100%)
Gene name: psaD
Sequence domains: PsaD
Photosystem I iron-sulfur center subunit VII Chain: E
Molecule details ›
Chain: E
Length: 94 amino acids
Theoretical weight: 10.55 KDa
Source organism: Cyanidioschyzon merolae strain 10D
UniProt:
  • Canonical: Q85FZ1 (Residues: 1-94; Coverage: 100%)
Gene name: psaE
Sequence domains: Photosystem I reaction centre subunit IV / PsaE
Structure domains: SH3 type barrels.
Photosystem I reaction center subunit III Chain: F
Molecule details ›
Chain: F
Length: 185 amino acids
Theoretical weight: 21.24 KDa
Source organism: Cyanidioschyzon merolae strain 10D
UniProt:
  • Canonical: Q85FS9 (Residues: 1-185; Coverage: 100%)
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 VIII Chain: I
Molecule details ›
Chain: I
Length: 32 amino acids
Theoretical weight: 3.41 KDa
Source organism: Cyanidioschyzon merolae strain 10D
UniProt:
  • Canonical: Q85FQ6 (Residues: 1-32; 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: 38 amino acids
Theoretical weight: 4.41 KDa
Source organism: Cyanidioschyzon merolae strain 10D
UniProt:
  • Canonical: Q85FS8 (Residues: 1-38; Coverage: 100%)
Gene name: psaJ
Sequence domains: Photosystem I reaction centre subunit IX / PsaJ
PSI-K Chain: K
Molecule details ›
Chain: K
Length: 60 amino acids
Theoretical weight: 6.3 KDa
Source organism: Cyanidioschyzon merolae strain 10D
UniProt:
  • Canonical: Q85G51 (Residues: 1-60; Coverage: 100%)
Gene name: psaK
Sequence domains: Photosystem I psaG / psaK
Photosystem I reaction center subunit XI Chain: L
Molecule details ›
Chain: L
Length: 140 amino acids
Theoretical weight: 15.16 KDa
Source organism: Cyanidioschyzon merolae strain 10D
UniProt:
  • Canonical: Q85FP8 (Residues: 1-140; Coverage: 100%)
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: Cyanidioschyzon merolae strain 10D
UniProt:
  • Canonical: Q85G73 (Residues: 1-29; Coverage: 100%)
Gene name: psaM
Sequence domains: Photosystem I protein M (PsaM)
Photosystem I subunit O Chain: O
Molecule details ›
Chain: O
Length: 155 amino acids
Theoretical weight: 16.74 KDa
Source organism: Cyanidioschyzon merolae strain 10D
UniProt:
  • Canonical: M1VFJ4 (Residues: 1-155; Coverage: 100%)
Gene name: CYME_CMP086C
Sequence domains: PsaO transmembrane domain

Ligands and Environments

11 bound ligands:
Ligand CLA 133 x CLA
Ligand ZEX 15 x ZEX
Ligand 1DO 1 x 1DO
Ligand CL0 1 x CL0
Ligand PQN 2 x PQN
Ligand LHG 2 x LHG
Ligand BCR 21 x BCR
Ligand SF4 3 x SF4
Ligand BGC 1 x BGC
Ligand DGD 1 x DGD
Ligand 3XQ 1 x 3XQ
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.82Å
Relevant EMDB volumes: EMD-6930

Quick links

Citations

10 review citations

Frontiers in Cryo Electron Microscopy of Complex Macromolecular Assemblies.
Ognjenović et al. (2019)
9 more

3 mentions without citation

Photosystem I: A Paradigm for Understanding Biological Environmental Adaptation Mechanisms in Cyanobacteria and Algae.
Tian et al. (2024)
2 more