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TitleVisualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes.
Journal, issue, pagesCell, Vol. 171, Issue 7, Page 1599-1610.e14, Year 2017
Publish dateDec 14, 2017
AuthorsLukas Kater / Matthias Thoms / Clara Barrio-Garcia / Jingdong Cheng / Sherif Ismail / Yasar Luqman Ahmed / Gert Bange / Dieter Kressler / Otto Berninghausen / Irmgard Sinning / Ed Hurt / Roland Beckmann /
PubMed AbstractEukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural ...Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural information, this process is poorly understood. Using cryo-EM, we solved structures of early 60S biogenesis intermediates at 3.3 Å to 4.5 Å resolution, thereby providing insights into their sequential folding and assembly pathway. Besides revealing distinct immature rRNA conformations, we map 25 assembly factors in six different assembly states. Notably, the Nsa1-Rrp1-Rpf1-Mak16 module stabilizes the solvent side of the 60S subunit, and the Erb1-Ytm1-Nop7 complex organizes and connects through Erb1's meandering N-terminal extension, eight assembly factors, three ribosomal proteins, and three 25S rRNA domains. Our structural snapshots reveal the order of integration and compaction of the six major 60S domains within early nucleolar 60S particles developing stepwise from the solvent side around the exit tunnel to the central protuberance.
External linksCell / PubMed:29245012 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.24 - 4.3 Å
Structure data

3888

6em3

EMDB-3888: State A (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
PDB-6em3: State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Method: EM (single particle) / Resolution: 4.2 Å

3889

6em4

EMDB-3889: State B (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
PDB-6em4: State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Method: EM (single particle) / Resolution: 4.1 Å

3890

6em5

EMDB-3890: State D (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
PDB-6em5: State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Method: EM (single particle) / Resolution: 4.2 Å

3891

6elz

EMDB-3891, PDB-6elz:
State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-3892:
State F (Rix1-TAP Rpf2-Flag) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Method: EM (single particle) / Resolution: 3.3 Å

3893

6em1

EMDB-3893, PDB-6em1:
State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Method: EM (single particle) / Resolution: 3.6 Å

PDB-6emf:
Crystal structure of Rrp1 from Chaetomium thermophilum in space group C2
Method: X-RAY DIFFRACTION / Resolution: 2.65 Å

PDB-6emg:
Crystal structure of Rrp1 from Chaetomium thermophilum in space group P6322
Method: X-RAY DIFFRACTION / Resolution: 2.24 Å

PDB-6en7:
Crystal structure of the ribosome assembly factor Nsa1
Method: X-RAY DIFFRACTION / Resolution: 2.403 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-PRO:
PROLINE / Proline

ChemComp-HOH:
WATER / Water

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-EPE:
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / pH buffer*YM / HEPES

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • saccharomyces cerevisiae s288c (yeast)
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
  • chaetomium thermophilum (strain dsm 1495 / cbs 144.50 / imi 039719) (fungus)
KeywordsRIBOSOME / Large Subunit Biogenesis Nucleolus / Ribosome biogenesis / translation / CHAPERONE / biogenesis

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