› 5y5s

X-ray diffraction
1.9Å resolution

Structure of photosynthetic LH1-RC super-complex at 1.9 angstrom resolution

Released:
DOI: 10.2210/pdb5y5s/pdb
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Source organism: Thermochromatium tepidum
Primary publication:
Structure of photosynthetic LH1-RC supercomplex at 1.9 Å resolution.
Yu LJ, Suga M, Wang-Otomo ZY, Shen JR
Nature 556 209-213 (2018)
PMID: 29618814

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 36-mer (preferred)
PDBe Complex ID:
PDB-CPX-108558 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
Photosynthetic reaction center cytochrome c subunit Chain: C
Molecule details ›
Chain: C
Length: 404 amino acids
Theoretical weight: 43.18 KDa
Source organism: Thermochromatium tepidum
UniProt:
  • Canonical: D2Z0P5 (Residues: 1-404; Coverage: 100%)
Gene name: pufC
Sequence domains: Photosynthetic reaction centre cytochrome C subunit
Structure domains: Photosynthetic Reaction Center, subunit C, domain 2
Reaction center protein L chain Chain: L
Molecule details ›
Chain: L
Length: 281 amino acids
Theoretical weight: 31.52 KDa
Source organism: Thermochromatium tepidum
UniProt:
  • Canonical: D2Z0P3 (Residues: 1-281; Coverage: 100%)
Gene name: pufL
Sequence domains: Photosynthetic reaction centre protein
Structure domains: Photosystem II protein D1-like
Reaction center protein M chain Chain: M
Photosynthetic reaction center H subunit Chain: H
Antenna complex alpha/beta subunit domain-containing protein Chains: 1, 3, 5, 7, 9, A, D, F, I, K, O, Q, S, U, W, Y
Antenna complex alpha/beta subunit domain-containing protein Chains: 0, 2, 4, 6, 8, B, E, G, J, N, P, R, T, V, X, Z

Ligands and Environments

18 bound ligands:
Ligand HEC 4 x HEC
Ligand MG 1 x MG
Ligand GOL 2 x GOL
Ligand SO4 3 x SO4
Ligand LHG 1 x LHG
Ligand PGV 10 x PGV
Ligand BCL 36 x BCL
Ligand BPH 2 x BPH
Ligand UQ8 5 x UQ8
Ligand UNL 16 x UNL
Ligand FE 1 x FE
Ligand MQ8 1 x MQ8
Ligand CRT 17 x CRT
Ligand PEF 13 x PEF
Ligand LDA 5 x LDA
Ligand CDL 9 x CDL
Ligand LMT 2 x LMT
Ligand CA 16 x CA
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: C2
Unit cell:
a: 145.28Å b: 143.81Å c: 210.28Å
α: 90° β: 90.74° γ: 90°
R-values:
R R work R free
0.183 0.181 0.215

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Citations

3 review citations

Novel features of LH1-RC from Thermochromatium tepidum revealed from its atomic resolution structure.
Yu et al. (2018)
2 more

19 mentions without citation

A comparative look at structural variation among RC-LH1 'Core' complexes present in anoxygenic phototrophic bacteria.
Gardiner et al. (2020)
18 more

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