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- PDB-6zqa: Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cere... -
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Basic information
Entry | Database: PDB / ID: 6zqa | ||||||
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Title | Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state A (Poly-Ala) | ||||||
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![]() | RIBOSOME / 90S pre-ribosome / 40S pre-ribosome / A1 cleavage / Dhr1 | ||||||
Function / homology | ![]() regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / RNA fragment catabolic process / rRNA 2'-O-methylation / CURI complex / UTP-C complex / nuclear microtubule / t-UTP complex / Mpp10 complex ...regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / RNA fragment catabolic process / rRNA 2'-O-methylation / CURI complex / UTP-C complex / nuclear microtubule / t-UTP complex / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / rRNA modification / regulation of rRNA processing / histone H2AQ104 methyltransferase activity / snRNA binding / tRNA re-export from nucleus / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / septum digestion after cytokinesis / regulation of transcription by RNA polymerase I / box C/D sno(s)RNA 3'-end processing / rDNA heterochromatin / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of rRNA processing / single-stranded telomeric DNA binding / U4/U6 snRNP / tRNA export from nucleus / rRNA base methylation / Negative regulators of DDX58/IFIH1 signaling / rRNA primary transcript binding / SUMOylation of RNA binding proteins / O-methyltransferase activity / protein localization to nucleolus / U4 snRNA binding / sno(s)RNA-containing ribonucleoprotein complex / box C/D methylation guide snoRNP complex / Protein hydroxylation / rRNA methylation / U4 snRNP / U3 snoRNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / poly(A)+ mRNA export from nucleus / preribosome, small subunit precursor / establishment of cell polarity / snoRNA binding / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / Major pathway of rRNA processing in the nucleolus and cytosol / spliceosomal complex assembly / SRP-dependent cotranslational protein targeting to membrane / nucleolar large rRNA transcription by RNA polymerase I / GTP hydrolysis and joining of the 60S ribosomal subunit / 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) / L13a-mediated translational silencing of Ceruloplasmin expression / proteasome assembly / 90S preribosome / regulation of translational fidelity / Ub-specific processing proteases / ribosomal subunit export from nucleus / RNA processing / ribosomal small subunit export from nucleus / 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) / U4/U6 x U5 tri-snRNP complex / enzyme activator activity / RNA endonuclease activity / Transferases; Transferring one-carbon groups; Methyltransferases / nuclear periphery / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / spliceosomal complex / maintenance of translational fidelity / mRNA splicing, via spliceosome / rRNA processing / unfolded protein binding / ribosome biogenesis / peroxisome / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||
![]() | Cheng, J. / Lau, B. / Venuta, G.L. / Berninghausen, O. / Hurt, E. / Beckmann, R. | ||||||
![]() | ![]() Title: 90 pre-ribosome transformation into the primordial 40 subunit. Authors: Jingdong Cheng / Benjamin Lau / Giuseppe La Venuta / Michael Ameismeier / Otto Berninghausen / Ed Hurt / Roland Beckmann / ![]() Abstract: Production of small ribosomal subunits initially requires the formation of a 90 precursor followed by an enigmatic process of restructuring into the primordial pre-40 subunit. We elucidate this ...Production of small ribosomal subunits initially requires the formation of a 90 precursor followed by an enigmatic process of restructuring into the primordial pre-40 subunit. We elucidate this process by biochemical and cryo-electron microscopy analysis of intermediates along this pathway in yeast. First, the remodeling RNA helicase Dhr1 engages the 90 pre-ribosome, followed by Utp24 endonuclease-driven RNA cleavage at site A, thereby separating the 5'-external transcribed spacer (ETS) from 18 ribosomal RNA. Next, the 5'-ETS and 90 assembly factors become dislodged, but this occurs sequentially, not en bloc. Eventually, the primordial pre-40 emerges, still retaining some 90 factors including Dhr1, now ready to unwind the final small nucleolar U3-18 RNA hybrid. Our data shed light on the elusive 90 to pre-40 transition and clarify the principles of assembly and remodeling of large ribonucleoproteins. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 3.5 MB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 11357MC ![]() 6zqbC ![]() 6zqcC ![]() 6zqdC ![]() 6zqeC ![]() 6zqfC ![]() 6zqgC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
+Protein , 15 types, 18 molecules UAUCUPUQCACBCFCGCMJFJGJHJJJNJOJPJQDF
+Nucleolar complex protein ... , 2 types, 2 molecules UBUS
+U3 small nucleolar RNA-associated protein ... , 16 types, 16 molecules UDUEUFUGUHUIUJUKULUMUNUOURUUUVCK
+RRNA-processing protein ... , 2 types, 2 molecules UXJM
+Ribosome biogenesis protein ... , 2 types, 2 molecules UZCL
+Nucleolar protein ... , 2 types, 2 molecules CDCE
+Ribosomal RNA-processing protein ... , 2 types, 2 molecules CHCN
+U3 small nucleolar ribonucleoprotein protein ... , 2 types, 2 molecules CICJ
+40S ribosomal protein ... , 11 types, 11 molecules DADHDJDNDODQDSDWDXDbDc
+RNA chain , 3 types, 3 molecules D2D3D4
+Non-polymers , 3 types, 5 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
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+Details
-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: 90S pre-ribbosome state A / Type: RIBOSOME / Entity ID: #1-#57 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil |
Vitrification | Cryogen name: ETHANE |
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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 | ||||||||||||
Image recording |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11194 / Symmetry type: POINT |