[English] 日本語
Yorodumi- PDB-4v8t: Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Ar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v8t | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1 | ||||||||||||
Components |
| ||||||||||||
Keywords | RIBOSOME / LARGE RIBOSOMAL SUBUNIT / RIBOSOME BIOGENESIS / RIBOSOME MATURATION FACTOR | ||||||||||||
Function / homology | Function and homology information Hydrolases / hexon binding / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / protein kinase activator activity / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) ...Hydrolases / hexon binding / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / protein kinase activator activity / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 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 / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / 90S preribosome / regulation of translational fidelity / protein-RNA complex assembly / ribonucleoprotein complex binding / translational termination / Neutrophil degranulation / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / translational initiation / macroautophagy / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing / protein tag activity / metallopeptidase activity / ribosome biogenesis / viral capsid / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / host cell nucleus / nucleolus / proteolysis / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.1 Å | ||||||||||||
Authors | Greber, B.J. / Boehringer, D. / Montellese, C. / Ban, N. | ||||||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2012 Title: Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit. Authors: Basil J Greber / Daniel Boehringer / Christian Montellese / Nenad Ban / Abstract: Eukaryotic ribosome biogenesis requires many protein factors that facilitate the assembly, nuclear export and final maturation of 40S and 60S particles. We have biochemically characterized ribosomal ...Eukaryotic ribosome biogenesis requires many protein factors that facilitate the assembly, nuclear export and final maturation of 40S and 60S particles. We have biochemically characterized ribosomal complexes of the yeast 60S-biogenesis factor Arx1 and late-maturation factors Rei1 and Jjj1 and determined their cryo-EM structures. Arx1 was visualized bound to the 60S subunit together with Rei1, at 8.1-Å resolution, to reveal the molecular details of Arx1 binding whereby Arx1 arrests the eukaryotic-specific rRNA expansion segment 27 near the polypeptide tunnel exit. Rei1 and Jjj1, which have been implicated in Arx1 recycling, bind in the vicinity of Arx1 and form a network of interactions. We suggest that, in addition to the role of Arx1 during pre-60S nuclear export, the binding of Arx1 conformationally locks the pre-60S subunit and inhibits the premature association of nascent chain-processing factors to the polypeptide tunnel exit. | ||||||||||||
History |
| ||||||||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "VB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "fA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4v8t.cif.gz | 3.2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4v8t.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v8t_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4v8t_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 4v8t_validation.xml.gz | 263.3 KB | Display | |
Data in CIF | 4v8t_validation.cif.gz | 433.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/4v8t ftp://data.pdbj.org/pub/pdb/validation_reports/v8/4v8t | HTTPS FTP |
-Related structure data
Related structure data | 2169MC 2167C 2168C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
+60S ribosomal protein ... , 40 types, 40 molecules ABCDEFGHIJKLMNPQRSTUVWXYZabcde...
-Large ribosomal subunit protein ... , 2 types, 2 molecules Oq
#15: Protein | Mass: 22247.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288C / References: UniProt: P26784 |
---|---|
#43: Protein | Mass: 33749.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288C / References: UniProt: P05317 |
-Protein , 2 types, 2 molecules mt
#39: Protein | Mass: 14583.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288C / References: UniProt: P0CH08 |
---|---|
#46: Protein | Mass: 67848.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-TERMINAL HIS-TAG / Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288C / Gene: ARX1, YDR101C, YD8557.10c / Plasmid: PPROEX-HTB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q03862, Hydrolases |
-RIBOSOMAL PROTEIN ... , 2 types, 2 molecules rs
#44: Protein | Mass: 14912.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast), (natural) Saccharomyces cerevisiae S288C (yeast) Strain: S288C / References: UniProt: P05318 |
---|---|
#45: Protein/peptide | Mass: 3932.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: S288C |
-RNA chain , 4 types, 4 molecules 1578
#47: RNA chain | Mass: 36810.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: S288C |
---|---|
#48: RNA chain | Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288C / References: GenBank: 834774822 |
#49: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288C / References: GenBank: 834774822 |
#50: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288C / References: GenBank: 940534893 |
-Non-polymers , 1 types, 4 molecules
#51: Chemical | ChemComp-ZN / |
---|
-Details
Sequence details | (1) THESE ARE PARTS OF THE PROTEIN SEQUENCES MODELED AS UNK RESIDUES. (2) THE MICROHETEROGENEITY ...(1) THESE ARE PARTS OF THE PROTEIN SEQUENCES MODELED AS UNK RESIDUES. (2) THE MICROHETER |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 60S RIBOSOMAL SUBUNIT IN COMPLEX WITH ARX1 AND REI1 / Type: RIBOSOME |
---|---|
Buffer solution | Name: 20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2 pH: 8 Details: 20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2 |
Specimen | Conc.: 0.16 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE Details: PLUNGE FREEZING IN LIQUID ETHANE AFTER MANUAL BLOTTING USING A MANUAL PLUNGE FREEZING DEVICE |
-Electron microscopy imaging
Microscopy | Model: FEI TECNAI 20 / Date: Feb 21, 2012 |
---|---|
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 83000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1500 nm / Cs: 2.3 mm |
Specimen holder | Temperature: 87 K / Tilt angle max: 0 ° |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Details: PER FRAME | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Method: PROJECTION MATCHING / Resolution: 8.1 Å / Num. of particles: 84113 / Nominal pixel size: 1.81 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2169. (DEPOSITION ID: 10977). Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--RIGID BODY | |||||||||||||||||||||
Atomic model building |
| |||||||||||||||||||||
Refinement | Highest resolution: 8.1 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 8.1 Å
|