› 6kad

Electron Microscopy
3.4Å resolution

Cryo-EM structure of the C2S2M2L2-type PSII-LHCII supercomplex from Chlamydomonas reihardtii

Released:
DOI: 10.2210/pdb6kad/pdb
PDB entry 6kad coloured by chain, front view.
PDB entry 6kad coloured by chain, side view.
PDB entry 6kad coloured by chain, top view.
Source organism: Chlamydomonas reinhardtii
Primary publication:
Structural insight into light harvesting for photosystem II in green algae.
Sheng X, Watanabe A, Li A, Kim E, Song C, Murata K, Song D, Minagawa J, Liu Z
Nat Plants 5 1320-1330 (2019)
PMID: 31768031
Related structures: EMD-9956

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 58-mer (preferred)
PDBe Complex ID:
PDB-CPX-108661 (preferred)
Entry contents:
23 distinct polypeptide molecules
Macromolecules (23 distinct):
Chlorophyll a-b binding protein, chloroplastic Chains: 0, 1, 6, 7, Y, y
Molecule details ›
Chains: 0, 1, 6, 7, Y, y
Length: 256 amino acids
Theoretical weight: 27.59 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q93VE0 (Residues: 1-256; Coverage: 100%)
Gene names: CHLRE_01g066917v5, LhcII-4, Lhcb
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chains: 2, 3, 5, 8, 9, N, n, p
Molecule details ›
Chains: 2, 3, 5, 8, 9, N, n, p
Length: 257 amino acids
Theoretical weight: 27.41 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q93WL4 (Residues: 1-257; Coverage: 100%)
Gene names: CHLRE_04g232104v5, LhcII-1.3
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chains: 4, G, g, q
Photosystem II protein D1 Chains: A, a
Photosystem II CP47 reaction center protein Chains: B, b
Photosystem II CP43 reaction center protein Chains: C, c
Photosystem II D2 protein Chains: D, d
Cytochrome b559 subunit alpha Chains: E, e
Cytochrome b559 subunit beta Chains: F, f
Photosystem II reaction center protein H Chains: H, h
Photosystem II reaction center protein I Chains: I, i
Photosystem II reaction center protein J Chains: J, j
Photosystem II reaction center protein K Chains: K, k
Photosystem II reaction center protein L Chains: L, l
Photosystem II reaction center protein M Chains: M, m
Oxygen-evolving enhancer protein 1, chloroplastic Chains: O, o
Chlorophyll a-b binding protein CP29 Chains: R, r
Chlorophyll a-b binding protein, chloroplastic Chains: S, s
Photosystem II reaction center protein T Chains: T, t
Photosystem II reaction center protein Ycf12 Chains: V, v
Photosystem II reaction center W protein, chloroplastic Chains: W, w
4.1 kDa photosystem II subunit Chains: X, x
Photosystem II reaction center protein Z Chains: Z, z

Ligands and Environments


Cofactor: Ligand HEM 2 x HEM
16 bound ligands:
Ligand CHL 122 x CHL
Ligand CLA 254 x CLA
Ligand LUT 42 x LUT
Ligand XAT 20 x XAT
Ligand NEX 22 x NEX
Ligand LHG 32 x LHG
Ligand OEX 2 x OEX
Ligand FE2 2 x FE2
Ligand CL 2 x CL
Ligand PHO 4 x PHO
Ligand BCR 20 x BCR
Ligand SQD 8 x SQD
Ligand LMG 14 x LMG
Ligand DGD 10 x DGD
Ligand BCT 2 x BCT
Ligand PL9 2 x PL9
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.4Å
Relevant EMDB volumes: EMD-9956

Quick links

Citations

7 review citations

Opportunities and challenges for assigning cofactors in cryo-EM density maps of chlorophyll-containing proteins.
Gisriel et al. (2020)
6 more

6 mentions without citation

Charting the native architecture of Chlamydomonas thylakoid membranes with single-molecule precision.
Wietrzynski et al. (2020)
5 more