+Open data
-Basic information
Entry | Database: PDB / ID: 3jct | ||||||
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Title | Cryo-em structure of eukaryotic pre-60S ribosomal subunits | ||||||
Components |
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Keywords | RIBOSOME / pre-60S ribosome | ||||||
Function / homology | Function and homology information protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / Hydrolases / PeBoW complex / 7S RNA binding / 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) ...protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / Hydrolases / PeBoW complex / 7S RNA binding / 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) / 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) / 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 / ribosomal large subunit binding / 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) / negative regulation of mRNA splicing, via spliceosome / nuclear-transcribed mRNA catabolic process / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / protein-RNA complex assembly / regulation of translational fidelity / ribosomal subunit export from nucleus / ribonucleoprotein complex binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Neutrophil degranulation / translation initiation factor activity / maturation of LSU-rRNA / proteasome complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / assembly of large subunit precursor of preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / ribosomal large subunit biogenesis / ribosomal large subunit assembly / maturation of SSU-rRNA / small-subunit processome / macroautophagy / maintenance of translational fidelity / protein catabolic process / rRNA processing / metallopeptidase activity / protein transport / ribosome biogenesis / ATPase binding / protein-macromolecule adaptor activity / 5S rRNA binding / large ribosomal subunit rRNA binding / nucleic acid binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / proteolysis / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å | ||||||
Authors | Wu, S. / Kumcuoglu, B. / Yan, K.G. / Brown, H. / Zhang, Y.X. / Tan, D. / Gamalinda, M. / Yuan, Y. / Li, Z.F. / Jakovljevic, J. ...Wu, S. / Kumcuoglu, B. / Yan, K.G. / Brown, H. / Zhang, Y.X. / Tan, D. / Gamalinda, M. / Yuan, Y. / Li, Z.F. / Jakovljevic, J. / Ma, C.Y. / Lei, J.L. / Dong, M.Q. / Woolford Jr., J.L. / Gao, N. | ||||||
Citation | Journal: Nature / Year: 2016 Title: Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomes. Authors: Shan Wu / Beril Tutuncuoglu / Kaige Yan / Hailey Brown / Yixiao Zhang / Dan Tan / Michael Gamalinda / Yi Yuan / Zhifei Li / Jelena Jakovljevic / Chengying Ma / Jianlin Lei / Meng-Qiu Dong / ...Authors: Shan Wu / Beril Tutuncuoglu / Kaige Yan / Hailey Brown / Yixiao Zhang / Dan Tan / Michael Gamalinda / Yi Yuan / Zhifei Li / Jelena Jakovljevic / Chengying Ma / Jianlin Lei / Meng-Qiu Dong / John L Woolford / Ning Gao / Abstract: Ribosome biogenesis is a highly complex process in eukaryotes, involving temporally and spatially regulated ribosomal protein (r-protein) binding and ribosomal RNA remodelling events in the ...Ribosome biogenesis is a highly complex process in eukaryotes, involving temporally and spatially regulated ribosomal protein (r-protein) binding and ribosomal RNA remodelling events in the nucleolus, nucleoplasm and cytoplasm. Hundreds of assembly factors, organized into sequential functional groups, facilitate and guide the maturation process into productive assembly branches in and across different cellular compartments. However, the precise mechanisms by which these assembly factors function are largely unknown. Here we use cryo-electron microscopy to characterize the structures of yeast nucleoplasmic pre-60S particles affinity-purified using the epitope-tagged assembly factor Nog2. Our data pinpoint the locations and determine the structures of over 20 assembly factors, which are enriched in two areas: an arc region extending from the central protuberance to the polypeptide tunnel exit, and the domain including the internal transcribed spacer 2 (ITS2) that separates 5.8S and 25S ribosomal RNAs. In particular, two regulatory GTPases, Nog2 and Nog1, act as hub proteins to interact with multiple, distant assembly factors and functional ribosomal RNA elements, manifesting their critical roles in structural remodelling checkpoints and nuclear export. Moreover, our snapshots of compositionally and structurally different pre-60S intermediates provide essential mechanistic details for three major remodelling events before nuclear export: rotation of the 5S ribonucleoprotein, construction of the active centre and ITS2 removal. The rich structural information in our structures provides a framework to dissect molecular roles of diverse assembly factors in eukaryotic ribosome assembly. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3jct.cif.gz | 3.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3jct.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 3jct.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jct_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3jct_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 3jct_validation.xml.gz | 282.5 KB | Display | |
Data in CIF | 3jct_validation.cif.gz | 483.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/3jct ftp://data.pdbj.org/pub/pdb/validation_reports/jc/3jct | HTTPS FTP |
-Related structure data
Related structure data | 6615MC 6616C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+60S ribosomal protein ... , 35 types, 35 molecules ABCDEFGHJLMNOPQRSTUVXYZacdefgh...
-Protein , 9 types, 9 molecules IKnswyz45
#9: Protein | Mass: 18546.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q08004 |
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#11: Protein | Mass: 42596.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38779 |
#40: Protein | Mass: 69984.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P53261 |
#45: Protein | Mass: 57798.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P40010 |
#49: Protein | Mass: 23001.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q08746 |
#51: Protein | Mass: 26476.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q12522 |
#52: Protein | Mass: 12435.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38202 |
#56: Protein | Mass: 65290.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q03862 |
#57: Protein | Mass: 14460.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P53188 |
-Ribosome assembly ... , 2 types, 2 molecules Wx
#23: Protein | Mass: 27098.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P33201 |
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#50: Protein | Mass: 57106.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P25382 |
-Nucleolar GTP-binding protein ... , 2 types, 2 molecules bm
#28: Protein | Mass: 74531.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q02892 |
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#39: Protein | Mass: 55585.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P53742 |
-Ribosome biogenesis protein ... , 6 types, 6 molecules oqrtuv
#41: Protein | Mass: 25499.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P53927 |
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#43: Protein | Mass: 52667.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q12080 |
#44: Protein | Mass: 29786.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P40078 |
#46: Protein | Mass: 36621.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P40693 |
#47: Protein | Mass: 24027.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q07915 |
#48: Protein | Mass: 39665.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P36160 |
-RNA chain , 4 types, 4 molecules 1236
#53: RNA chain | Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: GenBank: NR_132209.1 |
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#54: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: GenBank: NR_132211.1 |
#55: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: GenBank: NR_132224.1 |
#58: RNA chain | Mass: 74308.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: GenBank: NR_132210.1 |
-Non-polymers , 3 types, 8 molecules
#59: Chemical | ChemComp-ZN / #60: Chemical | #61: Chemical | |
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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: state1 of pre-60S ribosome subunit / Type: RIBOSOME |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Nov 7, 2015 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
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3D reconstruction | Resolution: 3.08 Å / Num. of particles: 191848 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Details: REFINEMENT PROTOCOL--rigid body | ||||||||||||
Atomic model building | PDB-ID: 4V88 Accession code: 4V88 / Source name: PDB / Type: experimental model | ||||||||||||
Refinement step | Cycle: LAST
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