› 8r2i

Electron Microscopy
2.9Å resolution

Cryo-EM Structure of native Photosystem II assembly intermediate from Chlamydomonas reinhardtii

Released:
DOI: 10.2210/pdb8r2i/pdb
PDB entry 8r2i coloured by chain, front view.
PDB entry 8r2i coloured by chain, side view.
PDB entry 8r2i coloured by chain, top view.
Source organism: Chlamydomonas reinhardtii
Primary publication:
Structure of native photosystem II assembly intermediate from Chlamydomonas reinhardtii.
Fadeeva M, Klaiman D, Kandiah E, Nelson N
Front Plant Sci 14 1334608 (2023)
PMID: 38322422
Related structures: EMD-18848

Function and Biology Details

Reaction catalysed: 
2 H(2)O + 2 plastoquinone + 4 light = O(2) + 2 plastoquinol
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
PDBe Complex ID:
PDB-CPX-239298 (preferred)
Entry contents:
11 distinct polypeptide molecules
Macromolecules (11 distinct):
Photosystem II protein D1 Chain: A
Molecule details ›
Chain: A
Length: 327 amino acids
Theoretical weight: 36.29 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P07753 (Residues: 11-337; Coverage: 93%)
Gene name: psbA
Sequence domains: Photosynthetic reaction centre protein
Photosystem II CP47 reaction center protein Chain: B
Molecule details ›
Chain: B
Length: 487 amino acids
Theoretical weight: 53.74 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P37255 (Residues: 2-488; Coverage: 96%)
Gene name: psbB
Sequence domains: Photosystem II protein
Photosystem II CP43 reaction center protein Chain: C
Molecule details ›
Chain: C
Length: 423 amino acids
Theoretical weight: 46.47 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P10898 (Residues: 21-443; Coverage: 92%)
Gene name: psbC
Sequence domains: Photosystem II protein
Photosystem II D2 protein Chain: D
Molecule details ›
Chain: D
Length: 350 amino acids
Theoretical weight: 39.24 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P06007 (Residues: 3-352; Coverage: 99%)
Gene name: psbD
Sequence domains: Photosynthetic reaction centre protein
Cytochrome b559 subunit alpha Chain: E
Molecule details ›
Chain: E
Length: 76 amino acids
Theoretical weight: 8.73 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P48268 (Residues: 7-82; Coverage: 93%)
Gene name: psbE
Sequence domains:
Cytochrome b559 subunit beta Chain: F
Molecule details ›
Chain: F
Length: 33 amino acids
Theoretical weight: 3.8 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q08363 (Residues: 12-44; Coverage: 75%)
Gene name: psbF
Sequence domains: Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits
Photosystem II reaction center protein H Chain: H
Molecule details ›
Chain: H
Length: 65 amino acids
Theoretical weight: 7.06 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P22666 (Residues: 19-83; Coverage: 74%)
Gene name: psbH
Sequence domains: Photosystem II 10 kDa phosphoprotein
Photosystem II reaction center protein I Chain: I
Molecule details ›
Chain: I
Length: 28 amino acids
Theoretical weight: 3.28 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P59763 (Residues: 1-28; Coverage: 76%)
Gene name: psbI
Sequence domains: Photosystem II reaction centre I protein (PSII 4.8 kDa protein)
Photosystem II reaction center protein K Chain: K
Molecule details ›
Chain: K
Length: 37 amino acids
Theoretical weight: 4.15 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P18263 (Residues: 10-46; Coverage: 80%)
Gene name: psbK
Sequence domains: Photosystem II 4 kDa reaction centre component
Chain U, Predicted protein Chain: 2
Molecule details ›
Chain: 2
Length: 101 amino acids
Theoretical weight: 11.21 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8I5A0 (Residues: 75-175; Coverage: 57%)
Gene name: CHLRE_05g243800v5
Sequence domains: Photosystem II Pbs27
Photosystem II reaction center protein Psb30 Chain: 1
Molecule details ›
Chain: 1
Length: 32 amino acids
Theoretical weight: 3.22 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P50370 (Residues: 1-32; Coverage: 97%)
Gene names: psb30, ycf12
Sequence domains: Photosystem II complex subunit Ycf12

Ligands and Environments


Cofactor: Ligand HEM 1 x HEM
11 bound ligands:
Ligand FE2 1 x FE2
Ligand CLA 35 x CLA
Ligand PHO 2 x PHO
Ligand BCR 8 x BCR
Ligand BOG 3 x BOG
Ligand LMG 2 x LMG
Ligand LMT 2 x LMT
Ligand LHG 1 x LHG
Ligand DGD 1 x DGD
Ligand BCT 1 x BCT
Ligand PL9 1 x PL9
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.9Å
Relevant EMDB volumes: EMD-18848

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