8C8L

In vitro structure of the Nitrosopumilus maritimus S-layer - Two-fold symmetry (C2)

Summary for 8C8L

• Entry DOI: 10.2210/pdb8c8l/pdb
• EMDB information: 16483
• Descriptor: Cell surface protein (1 entity in total)
• Functional Keywords: nmar_1547 s-layer, structural protein
• Biological source: Nitrosopumilus maritimus SCM1
• Total number of polymer chains: 6
• Total formula weight: 1098936.00

Authors

von Kuegelgen, A.,Bharat, T. (deposition date: 2023-01-20, release date: 2024-04-10, Last modification date: 2024-10-23)

Primary citation

von Kugelgen, A.,Cassidy, C.K.,van Dorst, S.,Pagani, L.L.,Batters, C.,Ford, Z.,Lowe, J.,Alva, V.,Stansfeld, P.J.,Bharat, T.A.M.
Membraneless channels sieve cations in ammonia-oxidizing marine archaea.
Nature, 630:230-236, 2024

PubMed Abstract: Nitrosopumilus maritimus is an ammonia-oxidizing archaeon that is crucial to the global nitrogen cycle. A critical step for nitrogen oxidation is the entrapment of ammonium ions from a dilute marine environment at the cell surface and their subsequent channelling to the cell membrane of N. maritimus. Here we elucidate the structure of the molecular machinery responsible for this process, comprising the surface layer (S-layer), using electron cryotomography and subtomogram averaging from cells. We supplemented our in situ structure of the ammonium-binding S-layer array with a single-particle electron cryomicroscopy structure, revealing detailed features of this immunoglobulin-rich and glycan-decorated S-layer. Biochemical analyses showed strong ammonium binding by the cell surface, which was lost after S-layer disassembly. Sensitive bioinformatic analyses identified similar S-layers in many ammonia-oxidizing archaea, with conserved sequence and structural characteristics. Moreover, molecular simulations and structure determination of ammonium-enriched specimens enabled us to examine the cation-binding properties of the S-layer, revealing how it concentrates ammonium ions on its cell-facing side, effectively acting as a multichannel sieve on the cell membrane. This in situ structural study illuminates the biogeochemically essential process of ammonium binding and channelling, common to many marine microorganisms that are fundamental to the nitrogen cycle.

PubMed: 38811725
DOI: 10.1038/s41586-024-07462-5

Experimental method

ELECTRON MICROSCOPY (2.71 Å)