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Yorodumi- EMDB-27919: Yeast co-transcriptional Noc1-Noc2 RNP assembly checkpoint interm... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27919 | |||||||||
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Title | Yeast co-transcriptional Noc1-Noc2 RNP assembly checkpoint intermediate | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Co-transcriptional pre-60S / ribosome biogenesis / early check-point intermediate / RIBOSOME | |||||||||
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 / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-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 | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Sanghai ZA / Piwowarczyk R / Vanden Broeck A / Klinge S | |||||||||
Funding support | United States, 2 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27919.map.gz | 301.7 MB | EMDB map data format | |
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Header (meta data) | emd-27919-v30.xml emd-27919.xml | 52.3 KB 52.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27919_fsc.xml | 15.6 KB | Display | FSC data file |
Images | emd_27919.png | 46.8 KB | ||
Filedesc metadata | emd-27919.cif.gz | 13.9 KB | ||
Others | emd_27919_half_map_1.map.gz emd_27919_half_map_2.map.gz | 301.2 MB 301.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27919 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27919 | HTTPS FTP |
-Validation report
Summary document | emd_27919_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_27919_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_27919_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | emd_27919_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27919 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27919 | HTTPS FTP |
-Related structure data
Related structure data | 8e5tMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27919.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_27919_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27919_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Yeast co-transcriptional ribosome assembly intermediate
+Supramolecule #1: Yeast co-transcriptional ribosome assembly intermediate
+Macromolecule #1: Ribosome biogenesis protein MAK21
+Macromolecule #2: NOC2 isoform 1
+Macromolecule #3: 60S ribosomal protein L4-A
+Macromolecule #4: Protein MAK16
+Macromolecule #5: 60S ribosomal protein L6-A
+Macromolecule #6: 60S ribosomal protein L7-A
+Macromolecule #7: 60S ribosomal protein L8-A
+Macromolecule #8: Proteasome-interacting protein CIC1
+Macromolecule #9: 60S ribosomal protein L13-A
+Macromolecule #10: 60S ribosomal protein L14-A
+Macromolecule #11: 60S ribosomal protein L15-A
+Macromolecule #12: 60S ribosomal protein L18-A
+Macromolecule #13: 60S ribosomal protein L20-A
+Macromolecule #14: Ribosome biogenesis protein BRX1
+Macromolecule #15: 60S ribosomal protein L32
+Macromolecule #16: 60S ribosomal protein L33-A
+Macromolecule #17: 60S ribosomal protein L36-A
+Macromolecule #18: rRNA-processing protein EBP2
+Macromolecule #19: Pescadillo homolog
+Macromolecule #20: Ribosome biogenesis protein 15
+Macromolecule #21: ATP-dependent RNA helicase HAS1
+Macromolecule #22: Ribosome biogenesis protein ERB1
+Macromolecule #23: Ribosome biogenesis protein RLP7
+Macromolecule #24: Ribosomal RNA-processing protein 1
+Macromolecule #25: 60S ribosomal protein L16-A
+Macromolecule #26: 25S ribosomal RNA
+Macromolecule #27: 5.8S ribosomal RNA
+Macromolecule #28: ITS2 ribosomal RNA
+Macromolecule #29: MAGNESIUM ION
+Macromolecule #30: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.6 |
Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.184 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |