› 5xnl

Electron Microscopy
2.7Å resolution

Structure of stacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum

Released:
DOI: 10.2210/pdb5xnl/pdb
PDB entry 5xnl coloured by chain, front view.
PDB entry 5xnl coloured by chain, side view.
PDB entry 5xnl coloured by chain, top view.
Source organism: Pisum sativum
Primary publication:
Structure and assembly mechanism of plant C2S2M2-type PSII-LHCII supercomplex.
Su X, Ma J, Wei X, Cao P, Zhu D, Chang W, Liu Z, Zhang X, Li M
Science 357 815-820 (2017)
PMID: 28839073
Related structures: EMD-6741

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 56-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-104183 (preferred)
Entry contents:
24 distinct polypeptide molecules
Macromolecules (24 distinct):
Chlorophyll a-b binding protein 8, chloroplastic Chains: 1, 2, 5, 6, G, N, Y, g, n, y
Molecule details ›
Chains: 1, 2, 5, 6, G, N, Y, g, n, y
Length: 232 amino acids
Theoretical weight: 24.95 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P27490 (Residues: 37-268; Coverage: 87%)
Gene names: CAB8, LHCB1
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chains: 3, 7
Molecule details ›
Chains: 3, 7
Length: 243 amino acids
Theoretical weight: 26.55 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q04918 (Residues: 23-265; Coverage: 92%)
Gene names: KIW84_056925, Lhcb3*1
Sequence domains: Chlorophyll A-B binding protein
Structure domains: Chlorophyll a/b binding protein domain
Chlorophyll a-b binding protein, chloroplastic Chains: 4, 8
Molecule details ›
Chains: 4, 8
Length: 210 amino acids
Theoretical weight: 22.86 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: A0A2D0TCJ3 (Residues: 1-210; Coverage: 100%)
Sequence domains: Chlorophyll A-B binding protein
Photosystem II protein D1 Chains: A, a
Molecule details ›
Chains: A, a
Length: 344 amino acids
Theoretical weight: 38.15 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P06585 (Residues: 1-344; Coverage: 98%)
Gene names: pgiI, psbA
Sequence domains: Photosynthetic reaction centre protein
Photosystem II CP47 reaction center protein Chains: B, b
Molecule details ›
Chains: B, b
Length: 507 amino acids
Theoretical weight: 56.12 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q9XQR6 (Residues: 1-507; Coverage: 100%)
Gene name: psbB
Sequence domains: Photosystem II protein
Structure domains: Photosystem II CP47 reaction center protein
Photosystem II CP43 reaction center protein Chains: C, c
Molecule details ›
Chains: C, c
Length: 473 amino acids
Theoretical weight: 52.04 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P06004 (Residues: 1-473; Coverage: 100%)
Gene name: psbC
Sequence domains: Photosystem II protein
Structure domains: photosystem ii from thermosynechococcus elongatus
Photosystem II D2 protein Chains: D, d
Molecule details ›
Chains: D, d
Length: 353 amino acids
Theoretical weight: 39.56 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P06006 (Residues: 1-353; Coverage: 100%)
Gene name: psbD
Sequence domains: Photosynthetic reaction centre protein
Cytochrome b559 subunit alpha Chains: E, e
Molecule details ›
Chains: E, e
Length: 83 amino acids
Theoretical weight: 9.42 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P13554 (Residues: 1-83; Coverage: 100%)
Gene name: psbE
Sequence domains:
Structure domains: Photosystem II cytochrome b559, alpha subunit
Cytochrome b559 subunit beta Chains: F, f
Molecule details ›
Chains: F, f
Length: 39 amino acids
Theoretical weight: 4.49 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P62096 (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, h
Molecule details ›
Chains: H, h
Length: 73 amino acids
Theoretical weight: 7.86 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q9XQR3 (Residues: 1-73; Coverage: 100%)
Gene name: psbH
Sequence domains: Photosystem II 10 kDa phosphoprotein
Structure domains: Photosystem II reaction center protein H
Photosystem II reaction center protein I Chains: I, i
Molecule details ›
Chains: I, i
Length: 36 amino acids
Theoretical weight: 4.18 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: D5MAJ9 (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, j
Molecule details ›
Chains: J, j
Length: 40 amino acids
Theoretical weight: 4.12 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P13555 (Residues: 1-40; Coverage: 100%)
Gene name: psbJ
Sequence domains: PsbJ
Photosystem II reaction center protein K Chains: K, k
Molecule details ›
Chains: K, k
Length: 61 amino acids
Theoretical weight: 6.91 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: D5MAJ8 (Residues: 1-61; 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: 4.5 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P60147 (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: Pisum sativum
UniProt:
  • Canonical: P69529 (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: 248 amino acids
Theoretical weight: 26.55 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P14226 (Residues: 82-329; Coverage: 75%)
Gene name: PSBO
Sequence domains: Manganese-stabilising protein / photosystem II polypeptide
Structure domains:
Oxygen-evolving enhancer protein 2, chloroplastic Chains: P, p
Molecule details ›
Chains: P, p
Length: 186 amino acids
Theoretical weight: 20.29 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P16059 (Residues: 74-259; Coverage: 72%)
Gene name: PSBP
Sequence domains:
Structure domains: Mog1/PsbP, alpha/beta/alpha sandwich
Oxygen-evolving enhancer protein 3-2 Chains: Q, q
Molecule details ›
Chains: Q, q
Length: 148 amino acids
Theoretical weight: 16.4 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q7Y1T5 (Residues: 87-234; Coverage: 63%)
Gene names: KIW84_046357, psbQ
Sequence domains: Oxygen evolving enhancer protein 3 (PsbQ)
Structure domains: Oxygen-evolving enhancer protein 3 (PsbQ), four-helix up-down bundle
Chlorophyll a-b binding protein, chloroplastic Chains: R, r
Molecule details ›
Chains: R, r
Length: 246 amino acids
Theoretical weight: 27.14 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: A0A2D0TCJ0 (Residues: 1-246; Coverage: 100%)
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chains: S, s
Molecule details ›
Chains: S, s
Length: 244 amino acids
Theoretical weight: 26.54 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: A0A2D0TCJ1 (Residues: 1-244; Coverage: 100%)
Sequence domains: Chlorophyll A-B binding protein
Structure domains: Chlorophyll a/b binding protein domain
Photosystem II reaction center protein T Chains: T, t
Molecule details ›
Chains: T, t
Length: 35 amino acids
Theoretical weight: 4.04 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q8HS25 (Residues: 1-35; Coverage: 100%)
Gene name: psbT
Sequence domains: Photosystem II reaction centre T protein
PSII 6.1 kDa protein Chains: W, w
Molecule details ›
Chains: W, w
Length: 54 amino acids
Theoretical weight: 5.91 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: A0A2D0TCJ2 (Residues: 1-54; Coverage: 100%)
Sequence domains: Photosystem II reaction centre W protein (PsbW)
Ultraviolet-B-repressible protein Chains: X, x
Molecule details ›
Chains: X, x
Length: 86 amino acids
Theoretical weight: 8.69 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q8VYY1 (Residues: 1-86; Coverage: 100%)
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: 6.56 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q32902 (Residues: 1-62; Coverage: 100%)
Gene names: psbZ, ycf9
Sequence domains: YCF9
Structure domains: Photosystem II PsbZ, reaction centre

Ligands and Environments


Cofactor: Ligand HEM 2 x HEM
16 bound ligands:
Ligand CHL 98 x CHL
Ligand CLA 216 x CLA
Ligand LUT 32 x LUT
Ligand XAT 16 x XAT
Ligand NEX 16 x NEX
Ligand LHG 36 x LHG
Ligand BCR 24 x BCR
Ligand OEX 2 x OEX
Ligand FE2 2 x FE2
Ligand CL 4 x CL
Ligand PHO 4 x PHO
Ligand SQD 8 x SQD
Ligand LMG 14 x LMG
Ligand PL9 4 x PL9
Ligand DGD 10 x DGD
Ligand BCT 2 x BCT
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.7Å
Relevant EMDB volumes: EMD-6741

Quick links

Citations

18 review citations

An online resource for GPCR structure determination and analysis.
Munk et al. (2019)
17 more

26 mentions without citation

Enhancing photosynthesis in plants: the light reactions.
Cardona et al. (2018)
25 more