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Structure paper

TitleStructural insights into assembly of the ribosomal nascent polypeptide exit tunnel.
Journal, issue, pagesNat Commun, Vol. 11, Issue 1, Page 5111, Year 2020
Publish dateOct 9, 2020
AuthorsDaniel M Wilson / Yu Li / Amber LaPeruta / Michael Gamalinda / Ning Gao / John L Woolford /
PubMed AbstractThe nascent polypeptide exit tunnel (NPET) is a major functional center of 60S ribosomal subunits. However, little is known about how the NPET is constructed during ribosome assembly. We utilized ...The nascent polypeptide exit tunnel (NPET) is a major functional center of 60S ribosomal subunits. However, little is known about how the NPET is constructed during ribosome assembly. We utilized molecular genetics, biochemistry, and cryo-electron microscopy (cryo-EM) to investigate the functions of two NPET-associated proteins, ribosomal protein uL4 and assembly factor Nog1, in NPET assembly. Structures of mutant pre-ribosomes lacking the tunnel domain of uL4 reveal a misassembled NPET, including an aberrantly flexible ribosomal RNA helix 74, resulting in at least three different blocks in 60S assembly. Structures of pre-ribosomes lacking the C-terminal extension of Nog1 demonstrate that this extension scaffolds the tunnel domain of uL4 in the NPET to help maintain stability in the core of pre-60S subunits. Our data reveal that uL4 and Nog1 work together in the maturation of ribosomal RNA helix 74, which is required to ensure proper construction of the NPET and 60S ribosomal subunits.
External linksNat Commun / PubMed:33037216 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 4.25 Å
Structure data

30170

7bt6

EMDB-30170, PDB-7bt6:
Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1)
Method: EM (single particle) / Resolution: 3.12 Å

EMDB-30172:
Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae nog1delta595-647rei1341-393reh1delta380-430 strain at 3.00 Angstroms resolution(state N1)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-30173:
Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae nog1delta595-647rei1341-393reh1delta380-430 strain at 4.25 Angstroms resolution(state N2)
Method: EM (single particle) / Resolution: 4.25 Å

30174

7btb

EMDB-30174, PDB-7btb:
Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2)
Method: EM (single particle) / Resolution: 3.22 Å

EMDB-30175:
Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae nog1delta595-647rei1341-393reh1delta380-430 strain at 3.77 Angstroms resolution(state N3)
Method: EM (single particle) / Resolution: 3.77 Å

EMDB-30176:
Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae nog1 delta595-647 rei1 delta341-393 reh1 delta380-430 strain at 4.21 Angstroms resolution(state N4)
Method: EM (single particle) / Resolution: 4.21 Å

Chemicals

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

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

Source
  • Saccharomyces cerevisiae S288C (yeast)
  • Baker's yeast (brewer's yeast)
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
KeywordsRIBOSOME / Pre-60s / rpl4

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