› 8bd3

Electron Microscopy
2.73Å resolution

Cryo-EM structure of the Photosystem II - LHCII supercomplex from Chlorella ohadi

Released:
DOI: 10.2210/pdb8bd3/pdb
PDB entry 8bd3 coloured by chain, front view.
PDB entry 8bd3 coloured by chain, side view.
PDB entry 8bd3 coloured by chain, top view.
Source organism: Chlorella ohadii
Primary publication:
Structure of Chlorella ohadii Photosystem II Reveals Protective Mechanisms against Environmental Stress.
Fadeeva M, Klaiman D, Caspy I, Nelson N
OpenAccess logo Cells 12 (2023)
PMID: 37566050
Related structures: EMD-15973

Function and Biology Details

Reactions catalysed: 
2 H(2)O + 2 plastoquinone + 4 light = O(2) + 2 plastoquinol
ATP + 1,2-diacyl-sn-glycerol = ADP + 1,2-diacyl-sn-glycerol 3-phosphate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 66-mer (preferred)
PDBe Complex ID:
PDB-CPX-224549 (preferred)
Entry contents:
29 distinct polypeptide molecules
Macromolecules (29 distinct):
Serine incorporator Chains: 1, 7
Molecule details ›
Chains: 1, 7
Length: 214 amino acids
Theoretical weight: 23.06 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: A0A2P6TPU9 (Residues: 563-776; Coverage: 19%)
Gene name: C2E21_5089
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding protein, chloroplastic Chains: 2, 4, 9, G, g, q
Molecule details ›
Chains: 2, 4, 9, G, g, q
Length: 222 amino acids
Theoretical weight: 23.85 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: A0A2P6TDA6 (Residues: 30-251; Coverage: 88%)
Gene name: C2E21_8827
Sequence domains: Chlorophyll A-B binding protein
Chlorophyll a-b binding of LHCII Chains: 3, 5, 8, N, n, p
Molecule details ›
Chains: 3, 5, 8, N, n, p
Length: 221 amino acids
Theoretical weight: 23.85 KDa
Source organism: Chlorella ohadii
Chlorophyll a-b binding of LHCII Chains: 0, 6
Molecule details ›
Chains: 0, 6
Length: 217 amino acids
Theoretical weight: 23.46 KDa
Source organism: Chlorella ohadii
Photosystem II protein D1 Chains: A, a
Molecule details ›
Chains: A, a
Length: 336 amino acids
Theoretical weight: 37.23 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: W8SIR2 (Residues: 9-344; Coverage: 95%)
Gene names: csorokcp_00030, psbA, psbA1
Sequence domains: Photosynthetic reaction centre protein
Photosystem II CP47 reaction center protein Chains: B, b
Molecule details ›
Chains: B, b
Length: 504 amino acids
Theoretical weight: 55.75 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: W8TIK4 (Residues: 2-505; Coverage: 99%)
Gene names: csorokcp_00052, psbB
Sequence domains: Photosystem II protein
Photosystem II CP43 reaction center protein Chains: C, c
Molecule details ›
Chains: C, c
Length: 448 amino acids
Theoretical weight: 49.16 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: A0A076EAP1 (Residues: 25-472; Coverage: 95%)
Gene name: psbC
Sequence domains: Photosystem II protein
Photosystem II D2 protein Chains: D, d
Molecule details ›
Chains: D, d
Length: 342 amino acids
Theoretical weight: 38.46 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: W8SYD4 (Residues: 11-352; Coverage: 97%)
Gene names: csorokcp_00092, psbD
Sequence domains: Photosynthetic reaction centre protein
Cytochrome b559 subunit alpha Chains: E, e
Molecule details ›
Chains: E, e
Length: 81 amino acids
Theoretical weight: 9.2 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: W8SU91 (Residues: 2-82; Coverage: 98%)
Gene names: csorokcp_00010, psbE
Sequence domains:
Cytochrome b559 subunit beta Chains: F, f
Molecule details ›
Chains: F, f
Length: 37 amino acids
Theoretical weight: 4.26 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: P56310 (Residues: 5-41; Coverage: 90%)
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: 67 amino acids
Theoretical weight: 7.22 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: W8SIT0 (Residues: 13-79; Coverage: 84%)
Gene names: csorokcp_00055, psbH
Sequence domains: Photosystem II 10 kDa phosphoprotein
Photosystem II reaction center protein I Chains: I, i
Molecule details ›
Chains: I, i
Length: 34 amino acids
Theoretical weight: 3.87 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: A0A5P4ND48 (Residues: 1-34; Coverage: 90%)
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: 38 amino acids
Theoretical weight: 3.81 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: W8TIH6 (Residues: 5-42; Coverage: 91%)
Gene names: csorokcp_00013, psbJ
Sequence domains: PsbJ
Photosystem II reaction center protein K Chains: K, k
Molecule details ›
Chains: K, k
Length: 37 amino acids
Theoretical weight: 4.14 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: P56348 (Residues: 6-42; Coverage: 88%)
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: 37 amino acids
Theoretical weight: 4.26 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: P56339 (Residues: 2-38; Coverage: 97%)
Gene name: psbL
Sequence domains: PsbL protein
Photosystem II reaction center protein M Chains: M, m
Molecule details ›
Chains: M, m
Length: 57 amino acids
Theoretical weight: 5.62 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: A0A5P4NAV9 (Residues: 1-32; Coverage: 94%)
Gene name: psbM
Sequence domains: Photosystem II reaction centre M protein (PsbM)
Chloroplast oxygen-evolving enhancer protein 1 Chains: O, o
Molecule details ›
Chains: O, o
Length: 240 amino acids
Theoretical weight: 25.45 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: A0A5P4NF37 (Residues: 52-291; Coverage: 83%)
Sequence domains: Manganese-stabilising protein / photosystem II polypeptide
Chlorophyll a b binding CP29 Chains: R, r
Molecule details ›
Chains: R, r
Length: 236 amino acids
Theoretical weight: 25.8 KDa
Source organism: Chlorella ohadii
Chlorophyll a b-binding CP26 Chains: S, s
Molecule details ›
Chains: S, s
Length: 257 amino acids
Theoretical weight: 27.37 KDa
Source organism: Chlorella ohadii
Photosystem II reaction center protein T Chains: T, t
Molecule details ›
Chains: T, t
Length: 30 amino acids
Theoretical weight: 3.48 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: P56327 (Residues: 1-30; Coverage: 97%)
Gene name: psbT
Sequence domains: Photosystem II reaction centre T protein
Photosystem II reaction center protein Psb30 Chains: V, v
Molecule details ›
Chains: V, v
Length: 32 amino acids
Theoretical weight: 3.32 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: A0A076EAR3 (Residues: 2-33; Coverage: 97%)
Gene names: psb30, ycf12
Sequence domains: Photosystem II complex subunit Ycf12
Photosystem II reaction center W protein Chains: W, w
Molecule details ›
Chains: W, w
Length: 60 amino acids
Theoretical weight: 6.62 KDa
Source organism: Chlorella ohadii
Photosystem II reaction center protein X Chains: X, x
Molecule details ›
Chains: X, x
Length: 37 amino acids
Theoretical weight: 3.53 KDa
Source organism: Chlorella ohadii
Multifunctional fusion protein Chains: Y, y
Molecule details ›
Chains: Y, y
Length: 221 amino acids
Theoretical weight: 23.86 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: A0A2P6U5M3 (Residues: 1419-1639; Coverage: 14%)
Gene name: C2E21_0264
Sequence domains: Chlorophyll A-B binding protein
Photosystem II reaction center protein Z Chains: Z, z
Molecule details ›
Chains: Z, z
Length: 62 amino acids
Theoretical weight: 6.73 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: W8SKL0 (Residues: 1-62; Coverage: 100%)
Gene names: csorokcp_00025, psbZ
Sequence domains: YCF9
Chloroplast oxygen-evolving enhancer protein 3 Chains: U, u
Molecule details ›
Chains: U, u
Length: 144 amino acids
Theoretical weight: 15.95 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: A0A5P4NB29 (Residues: 59-202; Coverage: 71%)
Sequence domains: Oxygen evolving enhancer protein 3
Chloroplast PsbY Chains: Q1, q1
Molecule details ›
Chains: Q1, q1
Length: 34 amino acids
Theoretical weight: 3.7 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: A0A5P4NEE0 (Residues: 322-355; Coverage: 9%)
Chloroplast photosystem II 10 kDa protein Chains: P1, p1
Molecule details ›
Chains: P1, p1
Length: 108 amino acids
Theoretical weight: 11.66 KDa
Source organism: Chlorella ohadii
UniProt:
  • Canonical: A0A5P4NAS4 (Residues: 32-139; Coverage: 77%)
Sequence domains: Photosystem II 10 kDa polypeptide PsbR
Photosystem II oxygen evolving enhancer 2 Chains: F1, f1
Molecule details ›
Chains: F1, f1
Length: 188 amino acids
Theoretical weight: 20.42 KDa
Source organism: Chlorella ohadii

Ligands and Environments


Cofactor: Ligand HEM 2 x HEM
18 bound ligands:
Ligand CHL 122 x CHL
Ligand CLA 270 x CLA
Ligand LUT 36 x LUT
Ligand LHG 44 x LHG
Ligand LMG 86 x LMG
Ligand RRX 6 x RRX
Ligand NEX 22 x NEX
Ligand XAT 8 x XAT
Ligand SQD 24 x SQD
Ligand OEX 2 x OEX
Ligand FE2 2 x FE2
Ligand CL 4 x CL
Ligand PHO 4 x PHO
Ligand BCR 22 x BCR
Ligand PL9 4 x PL9
Ligand DGD 8 x DGD
Ligand BCT 2 x BCT
Ligand LMU 4 x LMU
1 modified residue:
Ligand CSU 2 x CSU

Experiments and Validation Details

Entry percentile scores
Resolution: 2.73Å
Relevant EMDB volumes: EMD-15973

Quick links

Citations

4 mentions without citation

Evaluating Accuracy of DNA Pool Construction Based on White Blood Cell Counts.
Abrams et al. (2021)
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