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Yorodumi- PDB-8e5t: Yeast co-transcriptional Noc1-Noc2 RNP assembly checkpoint interm... -
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-Basic information
Entry | Database: PDB / ID: 8e5t | |||||||||
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Title | Yeast co-transcriptional Noc1-Noc2 RNP assembly checkpoint intermediate | |||||||||
Components |
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Keywords | RIBOSOME / Co-transcriptional pre-60S / ribosome biogenesis / early check-point intermediate | |||||||||
Function / homology | Function and homology information Noc1p-Noc2p complex / snoRNA release from pre-rRNA / Noc2p-Noc3p complex / 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) / PeBoW complex / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...Noc1p-Noc2p complex / snoRNA release from pre-rRNA / Noc2p-Noc3p complex / 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) / PeBoW complex / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / proteasome binding / maturation of 5.8S rRNA / 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 / 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 / preribosome, large subunit precursor / ribonucleoprotein complex binding / proteasome complex / nuclear periphery / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / macroautophagy / small-subunit processome / protein catabolic process / ribosomal large subunit assembly / rRNA processing / transcription corepressor activity / protein-macromolecule adaptor activity / nuclear envelope / ribosomal small subunit biogenesis / histone binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / rRNA binding / negative regulation of translation / ribosome / RNA helicase / structural constituent of ribosome / cell cycle / mRNA binding / nucleolus / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae BY4741 (yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | |||||||||
Authors | Sanghai, Z.A. / Piwowarczyk, R. / Vanden Broeck, A. / Klinge, S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: A co-transcriptional ribosome assembly checkpoint controls nascent large ribosomal subunit maturation. Authors: Zahra A Sanghai / Rafal Piwowarczyk / Arnaud Vanden Broeck / Sebastian Klinge / Abstract: During transcription of eukaryotic ribosomal DNA in the nucleolus, assembly checkpoints exist that guarantee the formation of stable precursors of small and large ribosomal subunits. While the ...During transcription of eukaryotic ribosomal DNA in the nucleolus, assembly checkpoints exist that guarantee the formation of stable precursors of small and large ribosomal subunits. While the formation of an early large subunit assembly checkpoint precedes the separation of small and large subunit maturation, its mechanism of action and function remain unknown. Here, we report the cryo-electron microscopy structure of the yeast co-transcriptional large ribosomal subunit assembly intermediate that serves as a checkpoint. The structure provides the mechanistic basis for how quality-control pathways are established through co-transcriptional ribosome assembly factors, that structurally interrogate, remodel and, together with ribosomal proteins, cooperatively stabilize correctly folded pre-ribosomal RNA. Our findings thus provide a molecular explanation for quality control during eukaryotic ribosome assembly in the nucleolus. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 8e5t.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8e5t.ent.gz | 1022 KB | Display | PDB format |
PDBx/mmJSON format | 8e5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8e5t_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8e5t_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8e5t_validation.xml.gz | 143.8 KB | Display | |
Data in CIF | 8e5t_validation.cif.gz | 241.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/8e5t ftp://data.pdbj.org/pub/pdb/validation_reports/e5/8e5t | HTTPS FTP |
-Related structure data
Related structure data | 27919MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Ribosome biogenesis protein ... , 5 types, 5 molecules 5bost
#1: Protein | Mass: 116832.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q12176 |
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#14: Protein | Mass: 33585.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q08235 |
#20: Protein | Mass: 25499.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P53927 |
#22: Protein | Mass: 91830.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q04660 |
#23: Protein | Mass: 36621.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P40693 |
-Protein , 7 types, 7 molecules 6DKmnpz
#2: Protein | Mass: 81719.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: A0A8H4BX61 |
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#4: Protein | Mass: 35754.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P10962 |
#8: Protein | Mass: 42596.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38779 |
#18: Protein | Mass: 49842.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P36049 |
#19: Protein | Mass: 69984.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P53261 |
#21: Protein | Mass: 56798.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q03532, RNA helicase |
#24: Protein | Mass: 33250.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P35178 |
-60S ribosomal protein ... , 13 types, 13 molecules CEFGLMNQSefiO
#3: Protein | Mass: 39159.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P10664 |
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#5: Protein | Mass: 20000.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q02326 |
#6: Protein | Mass: 27686.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P05737 |
#7: Protein | Mass: 28175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P17076 |
#9: Protein | Mass: 22604.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q12690 |
#10: Protein | Mass: 15195.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P36105 |
#11: Protein | Mass: 24482.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P05748 |
#12: Protein | Mass: 20609.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX49 |
#13: Protein | Mass: 20478.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX23 |
#15: Protein | Mass: 14809.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38061 |
#16: Protein | Mass: 12177.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P05744 |
#17: Protein | Mass: 11151.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P05745 |
#25: Protein | Mass: 22247.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P26784 |
-RNA chain , 3 types, 3 molecules 123
#26: RNA chain | Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: GenBank: 2211412803 |
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#27: RNA chain | Mass: 51012.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: GenBank: 1780004485 |
#28: RNA chain | Mass: 74308.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: GenBank: 1102641605 |
-Non-polymers , 2 types, 34 molecules
#29: Chemical | ChemComp-MG / #30: Chemical | ChemComp-ZN / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Yeast co-transcriptional ribosome assembly intermediate Type: COMPLEX / Entity ID: #1-#28 / Source: NATURAL |
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Molecular weight | Value: 0.8 MDa / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae BY4741 (yeast) |
Buffer solution | pH: 7.6 |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: PELCO Ultrathin Carbon with Lacey Carbon |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 1.184 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 32 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 158915 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6C0F Accession code: 6C0F / Source name: PDB / Type: experimental model |