› 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-501487 (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
Molecule details ›
Chains: 4, G, g, q
Length: 249 amino acids
Theoretical weight: 26.68 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q93WE0 (Residues: 1-249; Coverage: 100%)
Gene names: CHLRE_12g548400v5, LhcII-3
Sequence domains: Chlorophyll A-B binding protein
Photosystem II protein D1 Chains: A, a
Molecule details ›
Chains: A, 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 CP47 reaction center protein Chains: B, b
Molecule details ›
Chains: B, b
Length: 508 amino acids
Theoretical weight: 56.16 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P37255 (Residues: 1-508; Coverage: 100%)
Gene name: psbB
Sequence domains: Photosystem II protein
Photosystem II CP43 reaction center protein Chains: C, c
Molecule details ›
Chains: C, 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 D2 protein Chains: D, d
Molecule details ›
Chains: D, 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 Chains: E, e
Molecule details ›
Chains: E, 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 Chains: F, f
Molecule details ›
Chains: F, 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 Chains: H, h
Molecule details ›
Chains: H, 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 Chains: I, i
Molecule details ›
Chains: I, 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 J Chains: J, j
Molecule details ›
Chains: J, j
Length: 42 amino acids
Theoretical weight: 4.29 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: O19930 (Residues: 1-42; Coverage: 100%)
Gene name: psbJ
Sequence domains: PsbJ
Photosystem II reaction center protein K Chains: K, k
Molecule details ›
Chains: K, 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 Chains: L, l
Molecule details ›
Chains: L, 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 Chains: M, m
Molecule details ›
Chains: M, 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)
Oxygen-evolving enhancer protein 1, chloroplastic Chains: O, o
Molecule details ›
Chains: O, o
Length: 291 amino acids
Theoretical weight: 30.56 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: P12853 (Residues: 1-291; Coverage: 100%)
Gene name: PSBO
Sequence domains: Manganese-stabilising protein / photosystem II polypeptide
Chlorophyll a-b binding protein CP29 Chains: R, r
Molecule details ›
Chains: R, r
Length: 280 amino acids
Theoretical weight: 29.97 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q93WD2 (Residues: 1-280; Coverage: 100%)
Gene name: Lhcb4
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chains: S, s
Molecule details ›
Chains: S, s
Length: 289 amino acids
Theoretical weight: 30.74 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q9FEK6 (Residues: 1-289; Coverage: 100%)
Gene names: CHLRE_16g673650v5, lhcb5
Sequence domains: Chlorophyll A-B binding protein
Photosystem II reaction center protein T Chains: T, t
Molecule details ›
Chains: T, 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 Ycf12 Chains: V, v
Molecule details ›
Chains: V, v
Length: 33 amino acids
Theoretical weight: 3.33 KDa
Source organism: Chlamydomonas reinhardtii
Photosystem II reaction center W protein, chloroplastic Chains: W, w
Molecule details ›
Chains: W, w
Length: 115 amino acids
Theoretical weight: 12.16 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: Q9SPI9 (Residues: 1-115; Coverage: 100%)
Gene name: psbW
Sequence domains: Photosystem II reaction centre W protein (PsbW)
4.1 kDa photosystem II subunit Chains: X, x
Molecule details ›
Chains: X, 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 Chains: Z, z
Molecule details ›
Chains: Z, 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

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