Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Membraneless channels sieve cations in ammonia-oxidizing marine archaea.
Journal, issue, pages	Nature, Vol. 630, Issue 8015, Page 230-236, Year 2024
Publish date	May 29, 2024
Authors	Andriko von Kügelgen / C Keith Cassidy / Sofie van Dorst / Lennart L Pagani / Christopher Batters / Zephyr Ford / Jan Löwe / Vikram Alva / Phillip J Stansfeld / Tanmay A M Bharat /
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 ...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.
External links	Nature / PubMed:38811725 / PubMed Central
Methods	EM (single particle) / EM (subtomogram averaging)
Resolution	2.71 - 3.5 Å
Structure data	16482 8c8k EMDB-16482, PDB-8c8k: In vitro structure of the Nitrosopumilus maritimus S-layer - Six-fold symmetry (C6) Method: EM (single particle) / Resolution: 2.87 Å 16483 8c8l EMDB-16483, PDB-8c8l: In vitro structure of the Nitrosopumilus maritimus S-layer - Two-fold symmetry (C2) Method: EM (single particle) / Resolution: 2.71 Å 16484 8c8m EMDB-16484, PDB-8c8m: In vitro structure of the Nitrosopumilus maritimus S-layer - Composite map between two and six-fold symmetrised Method: EM (single particle) / Resolution: 2.87 Å 16487 8c8n EMDB-16487, PDB-8c8n: In situ structure of the Nitrosopumilus maritimus S-layer - Two-fold symmetry (C2) Method: EM (subtomogram averaging) / Resolution: 3.4 Å 16489 8c8o EMDB-16489, PDB-8c8o: In situ structure of the Nitrosopumilus maritimus S-layer - Six-fold symmetry (C6) Method: EM (subtomogram averaging) / Resolution: 3.4 Å 16492 8c8r EMDB-16492, PDB-8c8r: In situ structure of the Nitrosopumilus maritimus S-layer - Composite map between C2 and C6 Method: EM (subtomogram averaging) / Resolution: 3.5 Å
Source	nitrosopumilus maritimus scm1 (archaea)
Keywords	STRUCTURAL PROTEIN / Nmar_1547 S-layer