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› 8kde

Electron Microscopy
2.6Å resolution

Cryo-EM structure of an intermediate-state complex during the process of photosystem II repair

Released:
DOI: 10.2210/pdb8kde/pdb
PDB entry 8kde coloured by chain, front view.
PDB entry 8kde coloured by chain, side view.
PDB entry 8kde coloured by chain, top view.
Source organism: Chlamydomonas reinhardtii
Primary publication:
Structural basis for an early stage of the photosystem II repair cycle in Chlamydomonas reinhardtii.
Li A, You T, Pang X, Wang Y, Tian L, Li X, Liu Z
OpenAccess logo Nat Commun 15 5211 (2024)
PMID: 38890314
Related structures: EMD-37133

Function and Biology Details

Reaction catalysed: 
[2 a plastoquinone + 4 hnu + 2 H2O = 2 a plastoquinol + O2., 2 a plastoquinone + 4 hnu + 2 H2O = 2 a plastoquinol + O2.]
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
PDBe Complex ID:
PDB-CPX-269111 (preferred)
Entry contents:
18 distinct polypeptide molecules
Macromolecules (18 distinct):
Photosystem II CP47 reaction center protein Chain: B
Molecule details ›
Chain: B
Length: 508 amino acids
Theoretical weight: 56.09 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P37255 (Residues: 1-508; Coverage: 100%)
Gene name: psbB
Sequence domains: Photosystem II protein
Photosystem II D2 protein Chain: D
Molecule details ›
Chain: D
Length: 352 amino acids
Theoretical weight: 39.47 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P06007 (Residues: 1-352; Coverage: 100%)
Gene name: psbD
Sequence domains: Photosynthetic reaction centre protein
Cytochrome b559 subunit alpha Chain: E
Molecule details ›
Chain: E
Length: 82 amino acids
Theoretical weight: 9.31 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P48268 (Residues: 1-82; Coverage: 100%)
Gene name: psbE
Sequence domains:
Cytochrome b559 subunit beta Chain: F
Molecule details ›
Chain: F
Length: 44 amino acids
Theoretical weight: 4.99 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q08363 (Residues: 1-44; Coverage: 100%)
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: 88 amino acids
Theoretical weight: 9.45 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P22666 (Residues: 1-88; Coverage: 100%)
Gene name: psbH
Sequence domains: Photosystem II 10 kDa phosphoprotein
Photosystem II reaction center protein I Chain: I
Molecule details ›
Chain: I
Length: 37 amino acids
Theoretical weight: 4.25 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P59763 (Residues: 1-37; Coverage: 100%)
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: 46 amino acids
Theoretical weight: 5.06 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P18263 (Residues: 1-46; Coverage: 100%)
Gene name: psbK
Sequence domains: Photosystem II 4 kDa reaction centre component
Photosystem II reaction center protein L Chain: L
Molecule details ›
Chain: L
Length: 38 amino acids
Theoretical weight: 4.43 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P32974 (Residues: 1-38; Coverage: 100%)
Gene name: psbL
Sequence domains: PsbL protein
Photosystem II reaction center protein M Chain: M
Molecule details ›
Chain: M
Length: 34 amino acids
Theoretical weight: 3.76 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P92277 (Residues: 1-34; Coverage: 100%)
Gene name: psbM
Sequence domains: Photosystem II reaction centre M protein (PsbM)
Photosystem II reaction center protein T Chain: T
Molecule details ›
Chain: T
Length: 31 amino acids
Theoretical weight: 3.64 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P37256 (Residues: 1-31; Coverage: 100%)
Gene names: psbT, ycf8
Sequence domains: Photosystem II reaction centre T protein
Photosystem II reaction center protein Psb30 Chain: V
Molecule details ›
Chain: V
Length: 33 amino acids
Theoretical weight: 3.33 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P50370 (Residues: 1-33; Coverage: 100%)
Gene names: psb30, ycf12
Sequence domains: Photosystem II complex subunit Ycf12
Uncharacterized protein Chain: X
Molecule details ›
Chain: X
Length: 101 amino acids
Theoretical weight: 9.89 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8I846 (Residues: 1-101; Coverage: 100%)
Gene names: CHLRE_02g082750v5, CHLRE_02g082852v5
Sequence domains: Photosystem II reaction centre X protein (PsbX)
Photosystem II reaction center protein Z Chain: Z
Molecule details ›
Chain: Z
Length: 62 amino acids
Theoretical weight: 6.57 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P92276 (Residues: 1-62; Coverage: 100%)
Gene names: psbZ, ycf9
Sequence domains: YCF9
Maintenance of Photosystem II under High light 2 C-terminal domain-containing protein Chain: G
Molecule details ›
Chain: G
Length: 196 amino acids
Theoretical weight: 20.6 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8HY43 (Residues: 1-196; Coverage: 100%)
Gene name: CHLRE_06g256250v5
Sequence domains: Maintenance of Photosystem II under High light 2
Photosystem II repair factor 1 (PRF1) Chain: 3
Molecule details ›
Chain: 3
Length: 131 amino acids
Theoretical weight: 13.34 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3DWM2 (Residues: 1-131; Coverage: 100%)
Gene name: CHLRE_03g164300v5
Photosystem II CP43 reaction center protein Chain: C
Molecule details ›
Chain: C
Length: 461 amino acids
Theoretical weight: 50.68 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P10898 (Residues: 1-461; Coverage: 100%)
Gene name: psbC
Sequence domains: Photosystem II protein
Photosystem II protein D1 Chain: A
Molecule details ›
Chain: A
Length: 352 amino acids
Theoretical weight: 39.07 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P07753 (Residues: 1-352; Coverage: 100%)
Gene name: psbA
Sequence domains: Photosynthetic reaction centre protein
Photosystem II repair factor 2 (PRF2) Chain: 1
Molecule details ›
Chain: 1
Length: 117 amino acids
Theoretical weight: 12 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8HNG8 (Residues: 1-117; Coverage: 100%)
Gene name: CHLRE_01g051500v5

Ligands and Environments


Cofactor: Ligand HEM 1 x HEM
11 bound ligands:
Ligand CLA 35 x CLA
Ligand BCR 10 x BCR
Ligand LMG 6 x LMG
Ligand LHG 10 x LHG
Ligand PL9 1 x PL9
Ligand PHO 2 x PHO
Ligand VTQ 1 x VTQ
Ligand DGD 3 x DGD
Ligand SQD 1 x SQD
Ligand BCT 1 x BCT
Ligand FE2 1 x FE2
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.6Å
Relevant EMDB volumes: EMD-37133

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