+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2528 | |||||||||
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Title | Arx1 pre-60S particle | |||||||||
Map data | Cryo-EM reconstruction of an early yeast Arx1 pre-60S particle purified via Alb1-TAP. | |||||||||
Sample |
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Keywords | ribosome biogenesis / ribosome assembly / pre-60S / 5S RNP / assembly intermediate | |||||||||
Function / homology | Function and homology information protein-RNA complex remodeling / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Hydrolases / rRNA primary transcript binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / hexon binding / pre-mRNA 5'-splice site binding / maturation of 5.8S rRNA / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...protein-RNA complex remodeling / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Hydrolases / rRNA primary transcript binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / hexon binding / pre-mRNA 5'-splice site binding / maturation of 5.8S rRNA / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / ATPase activator activity / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / nuclear-transcribed mRNA catabolic process / translational elongation / ribosomal large subunit export from nucleus / regulation of translational fidelity / protein-RNA complex assembly / ribosomal subunit export from nucleus / Neutrophil degranulation / maturation of LSU-rRNA / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / assembly of large subunit precursor of preribosome / maturation of SSU-rRNA / cytosolic ribosome assembly / small-subunit processome / macroautophagy / maintenance of translational fidelity / rRNA processing / metallopeptidase activity / ribosome biogenesis / viral capsid / ribosomal large subunit assembly / ATPase binding / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / GTP binding / host cell nucleus / nucleolus / proteolysis / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.7 Å | |||||||||
Authors | Leidig C / Thoms M / Holdermann I / Bradatsch B / Berninghausen O / Bange G / Sinning I / Hurt E / Beckmann R | |||||||||
Citation | Journal: Nat Commun / Year: 2014 Title: 60S ribosome biogenesis requires rotation of the 5S ribonucleoprotein particle. Authors: Christoph Leidig / Matthias Thoms / Iris Holdermann / Bettina Bradatsch / Otto Berninghausen / Gert Bange / Irmgard Sinning / Ed Hurt / Roland Beckmann / Abstract: During eukaryotic ribosome biogenesis, nascent ribosomal RNA (rRNA) forms pre-ribosomal particles containing ribosomal proteins and assembly factors. Subsequently, these immature rRNAs are processed ...During eukaryotic ribosome biogenesis, nascent ribosomal RNA (rRNA) forms pre-ribosomal particles containing ribosomal proteins and assembly factors. Subsequently, these immature rRNAs are processed and remodelled. Little is known about the premature assembly states of rRNAs and their structural rearrangement during ribosome biogenesis. Using cryo-EM we characterize a pre-60S particle, where the 5S rRNA and its associated ribosomal proteins L18 and L5 (5S ribonucleoprotein (RNP)) are rotated by almost 180° when compared with the mature subunit. Consequently, neighbouring 25S rRNA helices that protrude from the base of the central protuberance are deformed. This altered topology is stabilized by nearby assembly factors (Rsa4 and Nog1), which were identified by fitting their three-dimensional structures into the cryo-EM density. We suggest that the 5S RNP performs a semicircular movement during 60S biogenesis to adopt its final position, fulfilling a chaperone-like function in guiding the flanking 25S rRNA helices of the central protuberance to their final topology. | |||||||||
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_2528.map.gz | 39.1 MB | EMDB map data format | |
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Header (meta data) | emd-2528-v30.xml emd-2528.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
Images | emd_2528.png | 176.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2528 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2528 | HTTPS FTP |
-Validation report
Summary document | emd_2528_validation.pdf.gz | 370.6 KB | Display | EMDB validaton report |
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Full document | emd_2528_full_validation.pdf.gz | 370.2 KB | Display | |
Data in XML | emd_2528_validation.xml.gz | 7.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2528 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2528 | HTTPS FTP |
-Related structure data
Related structure data | 4v7fMC 4nwbC 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_2528.map.gz / Format: CCP4 / Size: 264.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM reconstruction of an early yeast Arx1 pre-60S particle purified via Alb1-TAP. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0605 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 : TAP purification of Alb1-TAP from yeast.
Entire | Name: TAP purification of Alb1-TAP from yeast. |
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Components |
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-Supramolecule #1000: TAP purification of Alb1-TAP from yeast.
Supramolecule | Name: TAP purification of Alb1-TAP from yeast. / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Arx1 pre-60S particle
Supramolecule | Name: Arx1 pre-60S particle / type: complex / ID: 1 / Recombinant expression: No Ribosome-details: ribosome-eukaryote: LSU 60S, LSU RNA 28S, LSU RNA 5.8S, LSU RNA 5S |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV |
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-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Nov 12, 2012 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 5686 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | 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
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: OTHER / Number images used: 75887 |
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-Atomic model buiding 1
Initial model | PDB ID: 3u5d Chain - #0 - Chain ID: 1 / Chain - #1 - Chain ID: 3 / Chain - #2 - Chain ID: 4 |
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Details | The coordinates were initially fitted by rigid body fitting before the structure was manually adjusted to the density and refined using molecular dynamics simulations. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-4v7f: |
-Atomic model buiding 2
Initial model | PDB ID: 3u5e Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G / Chain - #7 - Chain ID: H / Chain - #8 - Chain ID: J / Chain - #9 - Chain ID: L / Chain - #10 - Chain ID: M / Chain - #11 - Chain ID: N / Chain - #12 - Chain ID: O / Chain - #13 - Chain ID: P / Chain - #14 - Chain ID: Q / Chain - #15 - Chain ID: R / Chain - #16 - Chain ID: S / Chain - #17 - Chain ID: T / Chain - #18 - Chain ID: U / Chain - #19 - Chain ID: V / Chain - #20 - Chain ID: X / Chain - #21 - Chain ID: Y / Chain - #22 - Chain ID: Z / Chain - #23 - Chain ID: a / Chain - #24 - Chain ID: c / Chain - #25 - Chain ID: d / Chain - #26 - Chain ID: e / Chain - #27 - Chain ID: f / Chain - #28 - Chain ID: g / Chain - #29 - Chain ID: h / Chain - #30 - Chain ID: i / Chain - #31 - Chain ID: j / Chain - #32 - Chain ID: k / Chain - #33 - Chain ID: l / Chain - #34 - Chain ID: p |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-4v7f: |
-Atomic model buiding 3
Initial model | PDB ID: 3izs Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: J |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-4v7f: |
-Atomic model buiding 4
Initial model | PDB ID: 4b6a Chain - Chain ID: t |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-4v7f: |