25HN

Cryo-EM structure of native Rubisco from Nitrosospira multiformis

Summary for 25HN

• Entry DOI: 10.2210/pdb25hn/pdb
• EMDB information: 80105
• Descriptor: Ribulose bisphosphate carboxylase large chain, Ribulose bisphosphate carboxylase small subunit, ZINC ION, ... (4 entities in total)
• Functional Keywords: rubisco, carbon fixation, nitrifying bacterium, autotrophy, cryo-em, lyase
• Biological source: Nitrosospira multiformis ATCC 25196; More
• Total number of polymer chains: 16
• Total formula weight: 570009.52

Authors

Tanaka, Y.,Nishigaya, Y. (deposition date: 2026-04-03, release date: 2026-05-27)

Primary citation

Tanaka, Y.,Nishigaya, Y.
Cryo-EM structure of RubisCO from Nitrosospira multiformis.
Biochem.Biophys.Res.Commun., 822:153886-153886, 2026

PubMed Abstract: Nitrosospira multiformis is a soil ammonia-oxidizing bacterium (AOB) that fixes CO via RubisCO using energy derived from ammonia oxidation. Despite its ecological and agricultural relevance, the structure of N. multiformis RubisCO (NmRubisCO) remained unknown. Here, we report the cryo-EM structure of NmRubisCO at 2.26 Å resolution, determined through single-particle analysis of protein copurified with the membrane fraction following cell lysis and ultracentrifugation without column chromatography. Analysis revealed an LS hexadecameric Form IC (red-like) RubisCO with a six-residue insertion in the βB-βC loop (BC loop) of the large-subunit N-terminal domain that forms a solvent-exposed, well-ordered protrusion. The active site lacks carbamylation at K206 and Mg binding, representing an inactive state. A putative metal ion coordinated by H296, H298, and H331, tentatively assigned as Zn based on coordination geometry and distances, was identified near the catalytic center; this His-coordinated metal site has not been described in other RubisCO structures. Loop 6 adopts a closed-like conformation in the absence of substrate, a configuration consistent with a potential requirement for activase-mediated remodeling. The C-terminal extension of the small subunit forms interdimer β-sheet interactions that stabilize the holoenzyme. These structural features provide a framework for understanding Form IC RubisCO in carboxysome-less soil AOB.

PubMed: 42127514
DOI: 10.1016/j.bbrc.2026.153886

Experimental method

ELECTRON MICROSCOPY (2.26 Å)