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- PDB-7ohv: Nog1-TAP associated immature ribosomal particles from S. cerevisi... -
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Basic information
Entry | Database: PDB / ID: 7ohv | ||||||
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Title | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C | ||||||
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![]() | RIBOSOME / ribosomal assembly state | ||||||
Function / homology | ![]() 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / snoRNA release from pre-rRNA / protein-RNA complex remodeling / 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) / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / PeBoW complex ...27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / snoRNA release from pre-rRNA / protein-RNA complex remodeling / 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) / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / PeBoW complex / ATP-dependent activity, acting on RNA / 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) / rRNA methylation / 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) / 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 / chromosome organization / 90S preribosome / protein-RNA complex assembly / regulation of translational fidelity / ribosomal subunit export from nucleus / ribonucleoprotein complex binding / 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 / maturation of SSU-rRNA / small-subunit processome / macroautophagy / maintenance of translational fidelity / protein catabolic process / rRNA processing / nuclear envelope / ribosomal small subunit biogenesis / protein-macromolecule adaptor activity / ATPase 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 / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
![]() | Milkereit, P. / Poell, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Analysis of subunit folding contribution of three yeast large ribosomal subunit proteins required for stabilisation and processing of intermediate nuclear rRNA precursors. Authors: Gisela Pöll / Michael Pilsl / Joachim Griesenbeck / Herbert Tschochner / Philipp Milkereit / ![]() Abstract: In yeast and human cells many of the ribosomal proteins (r-proteins) are required for the stabilisation and productive processing of rRNA precursors. Functional coupling of r-protein assembly with ...In yeast and human cells many of the ribosomal proteins (r-proteins) are required for the stabilisation and productive processing of rRNA precursors. Functional coupling of r-protein assembly with the stabilisation and maturation of subunit precursors potentially promotes the production of ribosomes with defined composition. To further decipher mechanisms of such an intrinsic quality control pathway we analysed here the contribution of three yeast large ribosomal subunit r-proteins rpL2 (uL2), rpL25 (uL23) and rpL34 (eL34) for intermediate nuclear subunit folding steps. Structure models obtained from single particle cryo-electron microscopy analyses provided evidence for specific and hierarchic effects on the stable positioning and remodelling of large ribosomal subunit domains. Based on these structural and previous biochemical data we discuss possible mechanisms of r-protein dependent hierarchic domain arrangement and the resulting impact on the stability of misassembled subunits. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 4.6 MB | Display | ![]() |
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PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 12910MC ![]() 7of1C ![]() 7oh3C ![]() 7ohpC ![]() 7ohqC ![]() 7ohrC ![]() 7ohsC ![]() 7ohtC ![]() 7ohuC ![]() 7ohwC ![]() 7ohxC ![]() 7ohyC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 4.9 TB Data #1: Unaligned multiframe micrographs of Nog1-TAP associated immature ribosomal particles from S. cerevisisae depleted of rpL2 [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 3 types, 3 molecules 126
#1: RNA chain | Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: GenBank: 834774822 |
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#2: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: RNA chain | Mass: 74308.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Ribosome biogenesis protein ... , 7 types, 7 molecules Amoprtu
#4: Protein | Mass: 33585.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q08235 |
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#37: Protein | Mass: 91830.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q04660 |
#39: Protein | Mass: 25499.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P53927 |
#40: Protein | Mass: 51426.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q12024 |
#41: Protein | Mass: 29786.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P40078 |
#42: Protein | Mass: 36621.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P40693 |
#43: Protein | Mass: 24027.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q07915 |
+60S ribosomal protein ... , 27 types, 27 molecules BCEFGHLMNOPQRSUVXYZadefhijk
-Protein , 9 types, 9 molecules DJKWbnvwy
#7: Protein | Mass: 56798.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q03532, RNA helicase |
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#12: Protein | Mass: 49842.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P36049 |
#13: Protein | Mass: 42596.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P38779 |
#24: Protein | Mass: 27098.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P33201 |
#29: Protein | Mass: 74531.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q02892 |
#38: Protein | Mass: 69984.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P53261 |
#44: Protein | Mass: 26954.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P40007 |
#45: Protein | Mass: 96656.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c References: UniProt: P25582, 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase |
#46: Protein | Mass: 26476.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q12522 |
-Non-polymers , 1 types, 1 molecules ![](data/chem/img/ZN.gif)
#47: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | N |
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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 |
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Sample preparation
Component | Name: Nog1-TAP associated immature ribosomal particles from cells depleted of rpL2. Type: RIBOSOME Details: Sample obtained from cellular extracts via affinity purification. Extracts were prepared from a rpL2 expression mutant strain. Entity ID: #1-#46 / Source: NATURAL | ||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / C2 aperture diameter: 70 µm |
Image recording | Average exposure time: 5.16 sec. / Electron dose: 86.45 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
Software | Name: UCSF ChimeraX / Version: 1.1/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19178 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6ELZ Accession code: 6ELZ / Source name: PDB / Type: experimental model |