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	Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits.
Journal, issue, pages	Nucleic Acids Res, Vol. 53, Issue 7, Year 2025
Publish date	Apr 10, 2025
Authors	Federica Fiorentino / Matthias Thoms / Klemens Wild / Timo Denk / Jingdong Cheng / Jakub Zeman / Irmgard Sinning / Ed Hurt / Roland Beckmann /
PubMed Abstract	The assembly of ribosomal subunits, primarily occurring in the nucleolar and nuclear compartments, is a highly complex process crucial for cellular function. This study reveals the conservation of ...The assembly of ribosomal subunits, primarily occurring in the nucleolar and nuclear compartments, is a highly complex process crucial for cellular function. This study reveals the conservation of ribosome biogenesis between yeast and humans, illustrated by the structural similarities of ribosomal subunit intermediates. By using X-ray crystallography and cryo-EM, the interaction between the human AAA+ ATPase MDN1 and the 60S assembly factor NLE1 is compared with the yeast homologs Rea1 and Rsa4. The MDN1-MIDAS and NLE1-Ubl complex structure at 2.3 Å resolution mirrors the highly conserved interaction patterns observed in yeast. Moreover, human pre-60S intermediates bound to the dominant negative NLE1-E85A mutant revealed at 2.8 Å resolution an architecture that largely matched the equivalent yeast structures. Conformation of rRNA, assembly factors and their interaction networks are highly conserved. Additionally, novel human pre-60S intermediates with a non-rotated 5S RNP and processed ITS2/foot structure but incomplete intersubunit surface were identified to be similar to counterparts observed in yeast. These findings confirm that the MDN1-NLE1-driven transition phase of the 60S assembly is essentially identical, supporting the idea that ribosome biogenesis is a highly conserved process across eukaryotic cells, employing an evolutionary preservation of ribosomal assembly mechanisms.
External links	Nucleic Acids Res / PubMed:40207627 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.3 - 7.88 Å
Structure data	EMDB-19287: Human pre-60S - State 6 - Consensus refinement Method: EM (single particle) / Resolution: 4.36 Å EMDB-19288: Human pre-60S - State 4 - Foot - local refinement Method: EM (single particle) / Resolution: 3.41 Å EMDB-19289: Human pre-60S - State 6 - RIX1 complex - local refinement Method: EM (single particle) / Resolution: 7.88 Å EMDB-19290: Human pre-60S - State 4 - GNL2 - local refinement Method: EM (single particle) / Resolution: 2.96 Å EMDB-19291: Human pre-60S - State 4 - 5S RNP - NLE1 - local refinement Method: EM (single particle) / Resolution: 3.43 Å EMDB-19292: Human pre-60S - State 4 - Consensus refinement Method: EM (single particle) / Resolution: 3.1 Å EMDB-19293: Human pre-60S - State 1D - Mask II - local refinement Method: EM (single particle) / Resolution: 4.21 Å EMDB-19294: Human pre-60S - State 1D - Mask I - local refinement Method: EM (single particle) / Resolution: 4.08 Å EMDB-19295: Human pre-60S - State 1D - GNL2 - local refinement Method: EM (single particle) / Resolution: 4.02 Å EMDB-19296: Human pre-60S - State 1D - 5S RNP - NLE1 - local refinement Method: EM (single particle) / Resolution: 4.25 Å EMDB-19297: Human pre-60S - State 1D - Consensus refinement Method: EM (single particle) / Resolution: 4.07 Å EMDB-19298: Human pre-60S - State 1C - Mask II - local refinement Method: EM (single particle) / Resolution: 3.62 Å EMDB-19299: Human pre-60S - State 1C - Mask I - local refinement Method: EM (single particle) / Resolution: 3.48 Å EMDB-19300: Human pre-60S - State 1C - GNL2 - local refinement Method: EM (single particle) / Resolution: 3.44 Å EMDB-19301: Human pre-60S - State 1C - 5S RNP - NLE1 - local refinement Method: EM (single particle) / Resolution: 3.71 Å EMDB-19302: Human pre-60S - State 1C - Consensus refinement Method: EM (single particle) / Resolution: 3.56 Å EMDB-19303: Human pre-60S - State 5 - MRTO4/uL11 - local refinement Method: EM (single particle) / Resolution: 2.86 Å EMDB-19304: Human pre-60S - State 5 - GNL2 - local refinement Method: EM (single particle) / Resolution: 2.71 Å EMDB-19305: Human pre-60S - State 5 - 5S RNP - NLE1 - local refinement Method: EM (single particle) / Resolution: 3.06 Å EMDB-19306: Human pre-60S - State 5 - Consensus refinement Method: EM (single particle) / Resolution: 2.84 Å EMDB-19307: Human pre-60S - State 3 - Mask - local refinement Method: EM (single particle) / Resolution: 3.12 Å EMDB-19308: Human pre-60S - State 3 - GNL2 - local refinement Method: EM (single particle) / Resolution: 2.97 Å EMDB-19309: Human pre-60S - State 3 - 5S RNP - NLE1 - local refinement Method: EM (single particle) / Resolution: 3.39 Å EMDB-19310: Human pre-60S - State 1A - Consensus refinement Method: EM (single particle) / Resolution: 3.04 Å EMDB-19311: Human pre-60S - State 2 - Mask - local refinement Method: EM (single particle) / Resolution: 3.26 Å EMDB-19312: Human pre-60S - State 2 - GNL2 - local refinement Method: EM (single particle) / Resolution: 3.02 Å EMDB-19313: Human pre-60S - State 2 - 5S RNP - NLE1 - local refinement Method: EM (single particle) / Resolution: 3.43 Å EMDB-19314: Human pre-60S - State 2 - Consensus refinement Method: EM (single particle) / Resolution: 3.1 Å EMDB-19315: Human pre-60S - State 1B - Mask II - local refinement Method: EM (single particle) / Resolution: 3.09 Å EMDB-19316: Human pre-60S - State 1B - Mask I - local refinement Method: EM (single particle) / Resolution: 3.08 Å EMDB-19317: Human pre-60S - State 1B - GNL2 - local refinement Method: EM (single particle) / Resolution: 3.04 Å EMDB-19318: Human pre-60S - State 1A - Mask II - local refinement Method: EM (single particle) / Resolution: 2.88 Å EMDB-19319: Human pre-60S - State 1B - 5S RNP - NLE1 - local refinement Method: EM (single particle) / Resolution: 3.29 Å EMDB-19320: Human pre-60S - State 1B - Consensus refinement Method: EM (single particle) / Resolution: 3.13 Å EMDB-19321: Human pre-60S - State 1A - Mask I - local refinement Method: EM (single particle) / Resolution: 2.87 Å EMDB-19322: Human pre-60S - State 1A - GNL2 - local refinement Method: EM (single particle) / Resolution: 2.84 Å EMDB-19323: Human pre-60S - State 1A - 5S RNP - NLE1 - local refinement Method: EM (single particle) / Resolution: 3.02 Å EMDB-19324: Human pre-60S - State 1A - Consensus refinement Method: EM (single particle) / Resolution: 2.9 Å EMDB-19325: Human pre-60S - State 7 Method: EM (single particle) / Resolution: 4.0 Å 19330 8rl2 EMDB-19330, PDB-8rl2: Human pre-60S - State 5 Method: EM (single particle) / Resolution: 2.84 Å 53196 9qiw EMDB-53196, PDB-9qiw: Human pre-60S - State 3 Method: EM (single particle) / Resolution: 3.04 Å PDB-8ql1: Crystal structure of the human MDN1-MIDAS/NLE1-UBL complex Method: X-RAY DIFFRACTION / Resolution: 2.3 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-HOH: WATER ChemComp-ZN: Unknown entry ChemComp-GTP: GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying moleculeYM ChemComp-GDP: GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying moleculeYM
Source	homo sapiens (human)
Keywords	RIBOSOME / AAA+ ATPase / Metal ion dependent adhesion site (MIDAS) / Ubiquitin-like domain (Ubl) / pre-60S biogenesis / Human / ribosome biogenesis / RIX1 complex / 5S RNP / NLE1