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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 / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit ...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 / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / preribosome, large subunit precursor / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / 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 / cytoplasm / cytosol
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_L15e / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal L15 / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / 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 S assembly.
Authors: Piwowarczyk, R. / Klinge, S.
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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