ISDA: 11AA

Deposition Date 2026-02-13

Release Date 2026-07-01

Last Version Date 2026-07-01

Entry Detail

PDB ID:

11AA

Keywords:

RIBOSOME

Title:

Yeast co-transcriptional pre-60S assembly intermediate Nop12 RNP

Biological Source:

Source Organism(s):

Saccharomyces cerevisiae S288C (Taxon ID: 559292)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.78 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:25S ribosomal RNA
Chain IDs:A (auth: 1)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:B (auth: 2)
Chain Length:159
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polyribonucleotide
Molecule:Internal transcribed spacer 2
Chain IDs:C (auth: 3)
Chain Length:232
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 16
Chain IDs:D (auth: 7)
Chain Length:231
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A
Chain IDs:E (auth: G)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 12
Chain IDs:F (auth: H)
Chain Length:459
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polypeptide(L)
Molecule:Proteasome-interacting protei
Chain IDs:G (auth: K)
Chain Length:376
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Chain IDs:H (auth: L)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15-A
Chain IDs:I (auth: N)
Chain Length:605
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein B
Chain IDs:J (auth: b)
Chain Length:291
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-A
Chain IDs:K (auth: i)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polypeptide(L)
Molecule:rRNA-processing protein EBP2
Chain IDs:L (auth: m)
Chain Length:427
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polypeptide(L)
Molecule:Pescadillo homolog
Chain IDs:M (auth: n)
Chain Length:605
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein 1
Chain IDs:N (auth: o)
Chain Length:220
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polypeptide(L)
Molecule:ATP-dependent RNA helicase HA
Chain IDs:O (auth: p)
Chain Length:505
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein E
Chain IDs:P (auth: s)
Chain Length:807
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein R
Chain IDs:Q (auth: t)
Chain Length:322
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Ligand Molecules

Primary Citation

Mechanism for the initiation of co-transcriptional pre-60 S assembly.

Piwowarczyk, R, Klinge, S.Show

Biorxiv ? ? ? (2026)

PMID: 42239465 DOI: 10.64898/2026.05.22.727207

Abstact

Eukaryotic ribosomal large subunit (60 S ) assembly requires an internal transcribed spacer 2 (ITS2) to license both nucleolar and nuclear pre-60 S assembly intermediates. The underlying molecular mechanisms responsible for nucleation of pre-60 S assembly, quality control, and installation of ITS2 during co-transcriptional stages remain unknown. Here we report the earliest co-transcriptional assembly intermediates of the eukaryotic 60 S subunits. Together with biochemical assays, our data reveal the architecture of co-transcriptional pre-60 S assembly initiation and progression, as well as the molecular logic of an assembly checkpoint. This study highlights an evolutionary solution by which complex RNA folding processes can be parallelized and integrated via biological AND-gating.

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Primary Citation of related structures

Abstact

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