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Structure paper

TitleVisualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
Journal, issue, pagesCell Res, Vol. 33, Issue 11, Page 867-878, Year 2023
Publish dateJul 25, 2023
AuthorsYunyang Zhang / Xiaomeng Liang / Sha Luo / Yan Chen / Yu Li / Chengying Ma / Ningning Li / Ning Gao /
PubMed AbstractEukaryotic ribosome assembly is a highly orchestrated process that involves over two hundred protein factors. After early assembly events on nascent rRNA in the nucleolus, pre-60S particles undergo ...Eukaryotic ribosome assembly is a highly orchestrated process that involves over two hundred protein factors. After early assembly events on nascent rRNA in the nucleolus, pre-60S particles undergo continuous maturation steps in the nucleoplasm, and prepare for nuclear export. Here, we report eleven cryo-EM structures of the nuclear pre-60S particles isolated from human cells through epitope-tagged GNL2, at resolutions of 2.8-4.3 Å. These high-resolution snapshots provide fine details for several major structural remodeling events at a virtual temporal resolution. Two new human nuclear factors, L10K and C11orf98, were also identified. Comparative structural analyses reveal that many assembly factors act as successive place holders to control the timing of factor association/dissociation events. They display multi-phasic binding properties for different domains and generate complex binding inter-dependencies as a means to guide the rRNA maturation process towards its mature conformation. Overall, our data reveal that nuclear assembly of human pre-60S particles is generally hierarchical with short branch pathways, and a few factors display specific roles as rRNA chaperones by confining rRNA helices locally to facilitate their folding, such as the C-terminal domain of SDAD1.
External linksCell Res / PubMed:37491604 / PubMed Central
MethodsEM (single particle)
Resolution2.8 - 4.3 Å
Structure data

EMDB-35370, PDB-8idt:
human nuclear pre-60S ribosomal particle - State G
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-35371, PDB-8idy:
human nuclear pre-60S ribosomal particle - State F
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-35375, PDB-8ie3:
human nuclear pre-60S ribosomal particle - State E
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-35596, PDB-8ine:
human nuclear pre-60S ribosomal particle - State G'
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-35597, PDB-8inf:
human nuclear pre-60S ribosomal particle - State F'
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-35599, PDB-8ink:
human nuclear pre-60S ribosomal particle - State D
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-35639, PDB-8ipd:
human nuclear pre-60S ribosomal particle - State C
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-35649, PDB-8ipx:
human nuclear pre-60S ribosomal particle - State C'
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-35651, PDB-8ipy:
human nuclear pre-60S ribosomal particle - State D'
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-35672, PDB-8ir1:
human nuclear pre-60S ribosomal particle - State A
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-35673, PDB-8ir3:
human nuclear pre-60S ribosomal particle - State B'
Method: EM (single particle) / Resolution: 3.5 Å

Chemicals

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

Source
  • homo sapiens (human)
KeywordsRIBOSOME / GNL2 / nuclear / pre-60S

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