8WDU image
Deposition Date 2023-09-16
Release Date 2024-02-21
Last Version Date 2024-11-13
Entry Detail
PDB ID:
8WDU
Keywords:
Title:
Photosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum purified by sucrose density
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.24 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Antenna complex alpha/beta subunit
Gene (Uniprot):Alvin_2547
Chain IDs:CA (auth: 3)
Chain Length:66
Number of Molecules:1
Biological Source:Allochromatium vinosum DSM 180
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Antenna complex alpha/beta subunit
Gene (Uniprot):Alvin_2549
Chain IDs:E (auth: A), K (auth: I), M (auth: K), O, Q, AA (auth: 1), EA (auth: 5), GA (auth: 7), IA (auth: 9)
Chain Length:44
Number of Molecules:9
Biological Source:Allochromatium vinosum DSM 180
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Antenna complex alpha/beta subunit
Gene (Uniprot):Alvin_2555
Chain IDs:F (auth: B), L (auth: J), N, P, R, BA (auth: 2), DA (auth: 4), FA (auth: 6), HA (auth: 8), JA (auth: 0)
Chain Length:46
Number of Molecules:10
Biological Source:Allochromatium vinosum DSM 180
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosynthetic reaction center cytochrome c subunit
Gene (Uniprot):pufC
Chain IDs:A (auth: C)
Chain Length:383
Number of Molecules:1
Biological Source:Allochromatium vinosum DSM 180
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Antenna complex alpha/beta subunit
Gene (Uniprot):Alvin_2554
Chain IDs:G (auth: D), I (auth: F), S, U, W, Y
Chain Length:64
Number of Molecules:6
Biological Source:Allochromatium vinosum DSM 180
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Antenna complex alpha/beta subunit
Gene (Uniprot):Alvin_2548
Chain IDs:H (auth: E), J (auth: G), T, V, X, Z
Chain Length:47
Number of Molecules:6
Biological Source:Allochromatium vinosum DSM 180
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosynthetic reaction center H subunit
Gene (Uniprot):Alvin_2637
Chain IDs:D (auth: H)
Chain Length:259
Number of Molecules:1
Biological Source:Allochromatium vinosum DSM 180
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Reaction center protein L chain
Gene (Uniprot):pufL
Chain IDs:B (auth: L)
Chain Length:278
Number of Molecules:1
Biological Source:Allochromatium vinosum DSM 180
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Reaction center protein M chain
Gene (Uniprot):pufM
Chain IDs:C (auth: M)
Chain Length:325
Number of Molecules:1
Biological Source:Allochromatium vinosum DSM 180
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
FME D MET modified residue
Primary Citation
High-resolution structure and biochemical properties of the LH1-RC photocomplex from the model purple sulfur bacterium, Allochromatium vinosum.
Commun Biol 7 176 176 (2024)
PMID: 38347078 DOI: 10.1038/s42003-024-05863-w

Abstact

The mesophilic purple sulfur phototrophic bacterium Allochromatium (Alc.) vinosum (bacterial family Chromatiaceae) has been a favored model for studies of bacterial photosynthesis and sulfur metabolism, and its core light-harvesting (LH1) complex has been a focus of numerous studies of photosynthetic light reactions. However, despite intense efforts, no high-resolution structure and thorough biochemical analysis of the Alc. vinosum LH1 complex have been reported. Here we present cryo-EM structures of the Alc. vinosum LH1 complex associated with reaction center (RC) at 2.24 Å resolution. The overall structure of the Alc. vinosum LH1 resembles that of its moderately thermophilic relative Alc. tepidum in that it contains multiple pigment-binding α- and β-polypeptides. Unexpectedly, however, six Ca ions were identified in the Alc. vinosum LH1 bound to certain α1/β1- or α1/β3-polypeptides through a different Ca2+-binding motif from that seen in Alc. tepidum and other Chromatiaceae that contain Ca2+-bound LH1 complexes. Two water molecules were identified as additional Ca2+-coordinating ligands. Based on these results, we reexamined biochemical and spectroscopic properties of the Alc. vinosum LH1-RC. While modest but distinct effects of Ca2+ were detected in the absorption spectrum of the Alc. vinosum LH1 complex, a marked decrease in thermostability of its LH1-RC complex was observed upon removal of Ca2+. The presence of Ca2+ in the photocomplex of Alc. vinosum suggests that Ca2+-binding to LH1 complexes may be a common adaptation in species of Chromatiaceae for conferring spectral and thermal flexibility on this key component of their photosynthetic machinery.

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Primary Citation of related structures
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