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- PDB-10zz: Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP* -

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Basic information

Entry
Database: PDB / ID: 10zz
TitleYeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP*
Components
  • (60S ribosomal protein ...) x 3
  • 25S ribosomal RNA
  • Periodic tryptophan protein 1
  • Ribosome biogenesis protein BRX1
  • rRNA-processing protein EBP2
KeywordsRIBOSOME / ribosome biogenesis / co-transcriptional assembly / RNA-binding protein / nucleolar RNP
Function / homology
Function and homology information


histone H4K20me3 reader activity / nuclear division / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / rRNA primary transcript binding / cytosolic large ribosomal subunit assembly / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / Major pathway of rRNA processing in the nucleolus and cytosol / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA ...histone H4K20me3 reader activity / nuclear division / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / rRNA primary transcript binding / cytosolic large ribosomal subunit assembly / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / Major pathway of rRNA processing in the nucleolus and cytosol / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / preribosome, large subunit precursor / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / maturation of LSU-rRNA / nuclear periphery / ribosomal large subunit biogenesis / rRNA processing / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / mRNA binding / nucleolus / RNA binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Periodic tryptophan protein 1 / Eukaryotic rRNA processing / Eukaryotic rRNA processing protein EBP2 / Ribosome biogenesis protein BRX1 / Brix domain / Brix domain / Brix domain profile. / Brix / Ribosomal protein L36e signature. / Ribosomal protein L7A/L8 ...Periodic tryptophan protein 1 / Eukaryotic rRNA processing / Eukaryotic rRNA processing protein EBP2 / Ribosome biogenesis protein BRX1 / Brix domain / Brix domain / Brix domain profile. / Brix / Ribosomal protein L36e signature. / Ribosomal protein L7A/L8 / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L15e, conserved site / Ribosomal protein L15e signature. / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal_L15e / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal L15 / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / WD domain, G-beta repeat / Ribosomal protein L23/L15e core domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL8A / Periodic tryptophan protein 1 / rRNA-processing protein EBP2 / Ribosome biogenesis protein BRX1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsPiwowarczyk, R. / Klinge, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM145950-03 United States
Chan Zuckerberg Initiative2023-332391 United States
CitationJournal: bioRxiv / Year: 2026
Title: Mechanism for the initiation of co-transcriptional pre-60 assembly.
Authors: Rafal Piwowarczyk / Sebastian Klinge
Abstract: Eukaryotic ribosomal large subunit (60 ) assembly requires an internal transcribed spacer 2 (ITS2) to license both nucleolar and nuclear pre-60 assembly intermediates. The underlying molecular ...Eukaryotic ribosomal large subunit (60 ) assembly requires an internal transcribed spacer 2 (ITS2) to license both nucleolar and nuclear pre-60 assembly intermediates. The underlying molecular mechanisms responsible for nucleation of pre-60 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 subunits. Together with biochemical assays, our data reveal the architecture of co-transcriptional pre-60 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.
History
DepositionFeb 13, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: 25S ribosomal RNA
G: 60S ribosomal protein L8-A
N: 60S ribosomal protein L15-A
R: Periodic tryptophan protein 1
b: Ribosome biogenesis protein BRX1
i: 60S ribosomal protein L36-A
m: rRNA-processing protein EBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,308,6529
Polymers1,308,6037
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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60S ribosomal protein ... , 3 types, 3 molecules GNi

#2: Protein 60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5


Mass: 28175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P17076
#3: Protein 60S ribosomal protein L15-A / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05748
#6: Protein 60S ribosomal protein L36-A / L39 / Large ribosomal subunit protein eL36-A / YL39


Mass: 11151.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05745

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Protein , 3 types, 3 molecules Rbm

#4: Protein Periodic tryptophan protein 1


Mass: 63872.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P21304
#5: Protein Ribosome biogenesis protein BRX1


Mass: 33585.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q08235
#7: Protein rRNA-processing protein EBP2 / EBNA1-binding protein homolog


Mass: 49842.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P36049

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RNA chain / Non-polymers , 2 types, 3 molecules 1

#1: RNA chain 25S ribosomal RNA


Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 831416132
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP
Type: RIBOSOME / Entity ID: #1-#7 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 51 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2crYOLOparticle selection
3SerialEMimage acquisition
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
14ISOLDEmodel refinement
15PHENIX1.19.1_4122model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: OTHER / Num. of particles: 242741 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 8E5T

8e5t


Accession code: 8E5T / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312647
ELECTRON MICROSCOPYf_angle_d0.57117708
ELECTRON MICROSCOPYf_dihedral_angle_d9.9682834
ELECTRON MICROSCOPYf_chiral_restr0.042068
ELECTRON MICROSCOPYf_plane_restr0.0041779

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