› 8z9d

Electron Microscopy
3.22Å resolution

cryo-EM structure of PSII-LHCII megacomplex from spinach

Released:
DOI: 10.2210/pdb8z9d/pdb
PDB entry 8z9d coloured by chain, front view.
PDB entry 8z9d coloured by chain, side view.
PDB entry 8z9d coloured by chain, top view.
Source organism: Spinacia oleracea
Entry authors: Shan JY, Liu ZF
Related structures: EMD-39860

Function and Biology Details

Reaction catalysed: 
2 H(2)O + 2 plastoquinone + 4 light = O(2) + 2 plastoquinol
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero 112-mer (preferred)
PDBe Complex ID:
PDB-CPX-498965 (preferred)
Entry contents:
28 distinct polypeptide molecules
Macromolecules (28 distinct):
Photosystem II protein D1 Chains: A, AA, Aa, a
Molecule details ›
Chains: A, AA, Aa, a
Length: 351 amino acids
Theoretical weight: 38.8 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P69560 (Residues: 1-351; Coverage: 99%)
Gene name: psbA
Sequence domains: Photosynthetic reaction centre protein
Oxygen-evolving enhancer protein 1, chloroplastic Chains: O, OO, Oo, o
Molecule details ›
Chains: O, OO, Oo, o
Length: 332 amino acids
Theoretical weight: 35.21 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P12359 (Residues: 1-332; Coverage: 100%)
Gene name: PSBO
Sequence domains: Manganese-stabilising protein / photosystem II polypeptide
Chlorophyll a-b binding protein, chloroplastic Chains: R, RR, Rr, r
Molecule details ›
Chains: R, RR, Rr, r
Length: 286 amino acids
Theoretical weight: 31.05 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: A0A9R0HRF2 (Residues: 1-286; Coverage: 100%)
Gene name: LOC110775011
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chains: S, SS, Ss, s
Molecule details ›
Chains: S, SS, Ss, s
Length: 295 amino acids
Theoretical weight: 31.34 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: A0A9R0IJF3 (Residues: 1-295; Coverage: 100%)
Gene name: LOC110790014
Sequence domains: Chlorophyll A-B binding protein
Photosystem II reaction center protein T Chains: T, TT, Tt, t
Molecule details ›
Chains: T, TT, Tt, t
Length: 33 amino acids
Theoretical weight: 3.83 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P61840 (Residues: 1-33; Coverage: 100%)
Gene names: psbT, ycf8
Sequence domains: Photosystem II reaction centre T protein
Photosystem II 5 kDa protein, chloroplastic Chains: U, UU, Uu, u
Molecule details ›
Chains: U, UU, Uu, u
Length: 99 amino acids
Theoretical weight: 10.68 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: A0A9R0J8H2 (Residues: 1-99; Coverage: 100%)
Gene name: LOC110801337
Photosystem II reaction center W protein, chloroplastic Chains: W, WW, Ww, w
Molecule details ›
Chains: W, WW, Ww, w
Length: 137 amino acids
Theoretical weight: 14.19 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q41387 (Residues: 1-137; Coverage: 100%)
Gene name: psbW
Sequence domains: Photosystem II reaction centre W protein (PsbW)
Photosystem II reaction center X protein, chloroplastic Chains: X, XX, Xx, x
Molecule details ›
Chains: X, XX, Xx, x
Length: 117 amino acids
Theoretical weight: 11.96 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: A0A9R0JQ89 (Residues: 1-117; Coverage: 100%)
Gene name: LOC110783121
Sequence domains: Photosystem II reaction centre X protein (PsbX)
Chlorophyll a-b binding protein, chloroplastic Chains: G, GG, Gg, N, NN, Nn, Y, YY, Yy, g, n, y
Molecule details ›
Chains: G, GG, Gg, N, NN, Nn, Y, YY, Yy, g, n, y
Length: 267 amino acids
Theoretical weight: 28.43 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: A0A9R0JBE4 (Residues: 1-267; Coverage: 100%)
Gene name: LOC110802314
Sequence domains: Chlorophyll A-B binding protein
Photosystem II reaction center protein Z Chains: Z, ZZ, Zz, z
Molecule details ›
Chains: Z, ZZ, Zz, z
Length: 62 amino acids
Theoretical weight: 6.54 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q9M3M6 (Residues: 1-62; Coverage: 100%)
Gene names: psbZ, ycf9
Sequence domains: YCF9
Chlorophyll a-b binding protein CP24, chloroplastic Chains: 4, 44
Molecule details ›
Chains: 4, 44
Length: 259 amino acids
Theoretical weight: 27.69 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P36494 (Residues: 1-259; Coverage: 99%)
Sequence domains: Chlorophyll A-B binding protein
Oxygen-evolving enhancer protein 2, chloroplastic Chains: P, PP, Pp, p
Molecule details ›
Chains: P, PP, Pp, p
Length: 267 amino acids
Theoretical weight: 28.5 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P12302 (Residues: 1-267; Coverage: 100%)
Gene name: PSBP
Sequence domains: PsbP
Oxygen-evolving enhancer protein 3, chloroplastic Chains: Q, QQ, Qq, q
Molecule details ›
Chains: Q, QQ, Qq, q
Length: 232 amino acids
Theoretical weight: 24.88 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P12301 (Residues: 1-232; Coverage: 100%)
Gene name: PSBQ
Sequence domains: Oxygen evolving enhancer protein 3
Chlorophyll a-b binding protein, chloroplastic Chains: 1, 11, 2, 22
Molecule details ›
Chains: 1, 11, 2, 22
Length: 267 amino acids
Theoretical weight: 28.43 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: A4F3R4 (Residues: 1-267; Coverage: 100%)
Gene names: LOC110789780, LOC110789782, lhcb1.1, lhcb1.1b
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chains: 3, 33
Molecule details ›
Chains: 3, 33
Length: 264 amino acids
Theoretical weight: 28.51 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: A0A9R0J656 (Residues: 1-264; Coverage: 100%)
Gene name: LOC110800942
Sequence domains: Chlorophyll A-B binding protein
Photosystem II 10 kDa polypeptide, chloroplastic Chains: 0, 00
Molecule details ›
Chains: 0, 00
Length: 140 amino acids
Theoretical weight: 14.41 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P10690 (Residues: 1-140; Coverage: 100%)
Gene name: PSBR
Sequence domains: Photosystem II 10 kDa polypeptide PsbR
Photosystem II reaction center proteins PsbY, chloroplastic Chains: 5, 55
Molecule details ›
Chains: 5, 55
Length: 199 amino acids
Theoretical weight: 20.68 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P80470 (Residues: 1-199; Coverage: 100%)
Gene name: PSBY
Sequence domains: Photosystem II protein Y (PsbY)
Photosystem II CP43 reaction center protein Chains: C, CC, Cc, c
Molecule details ›
Chains: C, CC, Cc, c
Length: 473 amino acids
Theoretical weight: 51.88 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P06003 (Residues: 1-473; Coverage: 100%)
Gene name: psbC
Sequence domains: Photosystem II protein
Photosystem II D2 protein Chains: D, DD, Dd, d
Molecule details ›
Chains: D, DD, Dd, d
Length: 352 amino acids
Theoretical weight: 39.42 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P06005 (Residues: 1-352; Coverage: 100%)
Gene name: psbD
Sequence domains: Photosynthetic reaction centre protein
Cytochrome b559 subunit alpha Chains: E, EE, Ee, e
Molecule details ›
Chains: E, EE, Ee, e
Length: 83 amino acids
Theoretical weight: 9.39 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P69383 (Residues: 1-83; Coverage: 100%)
Gene name: psbE
Sequence domains:
Cytochrome b559 subunit beta Chains: F, FF, Ff, f
Molecule details ›
Chains: F, FF, Ff, f
Length: 39 amino acids
Theoretical weight: 4.5 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P60128 (Residues: 1-39; 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, HH, Hh, h
Molecule details ›
Chains: H, HH, Hh, h
Length: 73 amino acids
Theoretical weight: 7.74 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P05146 (Residues: 1-73; Coverage: 100%)
Gene name: psbH
Sequence domains: Photosystem II 10 kDa phosphoprotein
Photosystem II reaction center protein I Chains: I, II, Ii, i
Molecule details ›
Chains: I, II, Ii, i
Length: 36 amino acids
Theoretical weight: 4.17 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P62103 (Residues: 1-36; 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, JJ, Jj, j
Molecule details ›
Chains: J, JJ, Jj, j
Length: 40 amino acids
Theoretical weight: 4.12 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q9M3L2 (Residues: 1-40; Coverage: 100%)
Gene name: psbJ
Sequence domains: PsbJ
Photosystem II reaction center protein K Chains: K, KK, Kk, k
Molecule details ›
Chains: K, KK, Kk, k
Length: 59 amino acids
Theoretical weight: 6.75 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P12163 (Residues: 1-59; Coverage: 100%)
Gene name: psbK
Sequence domains: Photosystem II 4 kDa reaction centre component
Photosystem II reaction center protein L Chains: L, LL, Ll, l
Molecule details ›
Chains: L, LL, Ll, l
Length: 38 amino acids
Theoretical weight: 4.5 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P60150 (Residues: 1-38; Coverage: 100%)
Gene name: psbL
Sequence domains: PsbL protein
Photosystem II reaction center protein M Chains: M, MM, Mm, m
Molecule details ›
Chains: M, MM, Mm, m
Length: 34 amino acids
Theoretical weight: 3.78 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P62112 (Residues: 1-34; Coverage: 100%)
Gene name: psbM
Sequence domains: Photosystem II reaction centre M protein (PsbM)
Photosystem II CP47 reaction center protein Chains: B, BB, Bb, b
Molecule details ›
Chains: B, BB, Bb, b
Length: 508 amino acids
Theoretical weight: 56.21 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P04160 (Residues: 1-508; Coverage: 100%)
Gene name: psbB
Sequence domains: Photosystem II protein

Ligands and Environments


Cofactor: Ligand HEM 4 x HEM
17 bound ligands:
Ligand OEX 4 x OEX
Ligand FE2 4 x FE2
Ligand CL 8 x CL
Ligand CLA 374 x CLA
Ligand PHO 8 x PHO
Ligand BCR 44 x BCR
Ligand PL9 6 x PL9
Ligand LHG 55 x LHG
Ligand SQD 14 x SQD
Ligand LMG 22 x LMG
Ligand CHL 140 x CHL
Ligand LUT 38 x LUT
Ligand XAT 18 x XAT
Ligand NEX 14 x NEX
Ligand LMU 4 x LMU
Ligand DGD 20 x DGD
Ligand BCT 4 x BCT
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.22Å
Relevant EMDB volumes: EMD-39860

Quick links