9KM0 image
Entry Detail
PDB ID:
9KM0
EMDB ID:
Keywords:
Title:
Cryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with EDTA-2Na-containing solutions
Biological Source:
PDB Version:
Deposition Date:
2024-11-15
Release Date:
2025-04-02
Method Details:
Experimental Method:
Resolution:
2.78 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Photosynthetic reaction center cytochrome c subunit
Chain IDs:MA (auth: C)
Chain Length:360
Number of Molecules:1
Biological Source:Dinoroseobacter shibae DFL 12 = DSM 16493
Polymer Type:polypeptide(L)
Description:Reaction center protein H chain
Chain IDs:LA (auth: H)
Chain Length:256
Number of Molecules:1
Biological Source:Dinoroseobacter shibae DFL 12 = DSM 16493
Polymer Type:polypeptide(L)
Description:Reaction center protein L chain
Chain IDs:KA (auth: L)
Chain Length:279
Number of Molecules:1
Biological Source:Dinoroseobacter shibae DFL 12 = DSM 16493
Polymer Type:polypeptide(L)
Description:Reaction center protein M chain
Chain IDs:JA (auth: M)
Chain Length:330
Number of Molecules:1
Biological Source:Dinoroseobacter shibae DFL 12 = DSM 16493
Polymer Type:polypeptide(L)
Description:Reaction center protein O chain
Chain IDs:B (auth: O)
Chain Length:239
Number of Molecules:1
Biological Source:Dinoroseobacter shibae DFL 12 = DSM 16493
Polymer Type:polypeptide(L)
Description:Antenna pigment protein alpha chain
Chain IDs:A (auth: P), C (auth: V), E (auth: S), G (auth: T), I (auth: Q), K (auth: R), O (auth: 1), Q (auth: N), S (auth: K), U (auth: J), W (auth: I), Y (auth: G), AA (auth: F), CA (auth: E), EA (auth: D), GA (auth: B), IA (auth: A)
Chain Length:53
Number of Molecules:17
Biological Source:Dinoroseobacter shibae DFL 12 = DSM 16493
Polymer Type:polypeptide(L)
Description:Antenna pigment protein beta chain
Chain IDs:D (auth: v), F (auth: t), H (auth: s), J (auth: r), L (auth: q), M (auth: p), N (auth: 2), P (auth: n), R (auth: k), T (auth: j), V (auth: i), X (auth: g), Z (auth: f), BA (auth: e), DA (auth: d), FA (auth: b), HA (auth: a)
Chain Length:49
Number of Molecules:17
Biological Source:Dinoroseobacter shibae DFL 12 = DSM 16493
Primary Citation
Cryo-EM Analysis of a Tri-Heme Cytochrome-Associated RC-LH1 Complex from the Marine Photoheterotrophic Bacterium Dinoroseobacter Shibae.
Adv Sci ? e2413456 e2413456 (2025)
PMID: 40112203 DOI: 10.1002/advs.202413456

Abstact

The reaction center-light harvesting 1 (RC-LH1) complex converts solar energy into electrical energy, driving the initiation of photosynthesis. The authors present a cryo-electron microscopy structure of the RC-LH1 isolated from a marine photoheterotrophic bacterium Dinoroseobacter shibae. The RC comprises four subunits, including a three-heme cytochrome (Cyt) c protein, and is surrounded by a closed LH ring composed of 17 pairs of antenna subunits. Notably, a novel subunit with an N-terminal "helix-turn-helix" motif embedded in the gap between the RC and the LH ring is identified. The purified RC-LH1 complex exhibits high stability in solutions containing Mg2+ or Ca2+. The periplasmic Cyt c2 is predicted to bind at the junction between the Cyt subunit and the membrane plane, enabling electron transfer from Cyt c2 to the proximal heme of the tri-heme Cyt, and subsequently to the special pair of bacteriochlorophylls. These findings provide structural insights into the efficient energy and electron transfer processes within a distinct type of RC-LH1, and shed light on evolutionary adaptations of photosynthesis.

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