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Yorodumi- EMDB-5513: Structure of late pre-60S ribosomal subunits with nuclear export ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5513 | |||||||||
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Title | Structure of late pre-60S ribosomal subunits with nuclear export factor Arx1 bound at the peptide exit tunnel | |||||||||
Map data | Reconstruction of pre-60S ribosomal subunits with nuclear export factor Arx1 bound at the peptide exit tunnel | |||||||||
Sample |
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Keywords | ribosome pre-ribosome pre-60S factors | |||||||||
Function / homology | Function and homology information maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / ribosomal large subunit binding / preribosome, large subunit precursor / ribosomal subunit export from nucleus / translation initiation factor activity / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly ...maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / ribosomal large subunit binding / preribosome, large subunit precursor / ribosomal subunit export from nucleus / translation initiation factor activity / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit biogenesis / positive regulation of cell differentiation / rRNA processing / transcription corepressor activity / azurophil granule lumen / regulation of translation / nucleic acid binding / ribonucleoprotein complex / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / Neutrophil degranulation / negative regulation of apoptotic process / nucleolus / RNA binding / extracellular exosome / extracellular region / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.9 Å | |||||||||
Authors | Bradatsch B / Leidig C / Granneman S / Gnaedig M / Tollervey D / Boettcher B / Beckmann R / Hurt E | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2012 Title: Structure of the pre-60S ribosomal subunit with nuclear export factor Arx1 bound at the exit tunnel. Authors: Bettina Bradatsch / Christoph Leidig / Sander Granneman / Marén Gnädig / David Tollervey / Bettina Böttcher / Roland Beckmann / Ed Hurt / Abstract: Preribosomal particles evolve in the nucleus through transient interaction with biogenesis factors before export to the cytoplasm. Here, we report the architecture of the late pre-60S particle, ...Preribosomal particles evolve in the nucleus through transient interaction with biogenesis factors before export to the cytoplasm. Here, we report the architecture of the late pre-60S particle, purified from Saccharomyces cerevisiae, through Arx1, a nuclear export factor with structural homology to methionine aminopeptidases, or its binding partner Alb1. Cryo-EM reconstruction of the Arx1 particle at 11.9-Å resolution reveals regions of extra density on the pre-60S particle attributed to associated biogenesis factors, confirming the immature state of the nascent subunit. One of these densities could be unambiguously assigned to Arx1. Immunoelectron microscopy and UV cross-linking localize Arx1 close to the ribosomal exit tunnel, in direct contact with ES27, a highly dynamic eukaryotic rRNA expansion segment. The binding of Arx1 at the exit tunnel may position this export factor to prevent premature recruitment of ribosome-associated factors active during translation. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5513.map.gz | 22.7 MB | EMDB map data format | |
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Header (meta data) | emd-5513-v30.xml emd-5513.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | emd_5513.png | 636.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5513 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5513 | HTTPS FTP |
-Validation report
Summary document | emd_5513_validation.pdf.gz | 354.3 KB | Display | EMDB validaton report |
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Full document | emd_5513_full_validation.pdf.gz | 353.9 KB | Display | |
Data in XML | emd_5513_validation.xml.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5513 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5513 | HTTPS FTP |
-Related structure data
Related structure data | 3j2iMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5513.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of pre-60S ribosomal subunits with nuclear export factor Arx1 bound at the peptide exit tunnel | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2375 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : pre-60S particle
Entire | Name: pre-60S particle |
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Components |
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-Supramolecule #1000: pre-60S particle
Supramolecule | Name: pre-60S particle / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Experimental: 1.3 MDa / Theoretical: 1.3 MDa |
-Supramolecule #1: Pre-60S particle
Supramolecule | Name: Pre-60S particle / type: complex / ID: 1 / Name.synonym: pre-60S / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-eukaryote: LSU 60S |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: yeast |
-Macromolecule #1: Proliferation-associated protein 2G4
Macromolecule | Name: Proliferation-associated protein 2G4 / type: protein_or_peptide / ID: 1 / Name.synonym: Ebp1 / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Homo sapiens (human) / synonym: human |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 Details: 50 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1.5 mM or 5 mM MgCl2, 0.075% (v/v) NP-40 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 2 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Apr 6, 2012 |
Image recording | Category: CCD / Film or detector model: GENERIC CCD / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 95000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | The particles were selected using an automatic selection program |
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CTF correction | Details: Subvolumes |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Signature, Spider, Chimera / Number images used: 100000 |