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- PDB-5oql: Cryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum -
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Open data
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Basic information
Entry | Database: PDB / ID: 5oql | ||||||
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Title | Cryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum | ||||||
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![]() | RIBOSOME / Ribosome biogenesis | ||||||
Function / homology | ![]() rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA N-acetyltransferase activity / tRNA acetylation / Noc4p-Nop14p complex / tRNA wobble cytosine modification / t-UTP complex / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity ...rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA N-acetyltransferase activity / tRNA acetylation / Noc4p-Nop14p complex / tRNA wobble cytosine modification / t-UTP complex / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / histone H2AQ104 methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA 3'-end processing / 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 / rRNA primary transcript binding / rRNA base methylation / sno(s)RNA-containing ribonucleoprotein complex / box C/D methylation guide snoRNP complex / U3 snoRNA binding / snoRNA binding / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / RNA nuclease activity / RNA processing / Cajal body / U4/U6 x U5 tri-snRNP complex / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RNA endonuclease activity / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / methyltransferase activity / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / rRNA processing / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / methylation / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / RNA binding / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
![]() | Cheng, J. / Kellner, N. / Berninghausen, O. / Hurt, E. / Beckmann, R. | ||||||
![]() | ![]() Title: 3.2-Å-resolution structure of the 90S preribosome before A1 pre-rRNA cleavage. Authors: Jingdong Cheng / Nikola Kellner / Otto Berninghausen / Ed Hurt / Roland Beckmann / ![]() Abstract: The 40S small ribosomal subunit is cotranscriptionally assembled in the nucleolus as part of a large chaperone complex called the 90S preribosome or small-subunit processome. Here, we present the 3.2- ...The 40S small ribosomal subunit is cotranscriptionally assembled in the nucleolus as part of a large chaperone complex called the 90S preribosome or small-subunit processome. Here, we present the 3.2-Å-resolution structure of the Chaetomium thermophilum 90S preribosome, which allowed us to build atomic structures for 34 assembly factors, including the Mpp10 complex, Bms1, Utp14 and Utp18, and the complete U3 small nucleolar ribonucleoprotein. Moreover, we visualized the U3 RNA heteroduplexes with a 5' external transcribed spacer (5' ETS) and pre-18S RNA, and their stabilization by 90S factors. Overall, the structure explains how a highly intertwined network of assembly factors and pre-rRNA guide the sequential, independent folding of the individual pre-40S domains while the RNA regions forming the 40S active sites are kept immature. Finally, by identifying the unprocessed A1 cleavage site and the nearby Utp24 endonuclease, we suggest a proofreading model for regulated 5'-ETS separation and 90S-pre-40S transition. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.2 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 328.7 KB | Display | |
Data in CIF | ![]() | 552.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3847MC 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 , 32 types, 36 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZadef...
-Putative U3 small nucleolar ... , 2 types, 2 molecules bc
#26: Protein | Mass: 34216.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0SE90 |
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#27: Protein | Mass: 86082.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0S9I7 |
-40S ribosomal protein ... , 15 types, 15 molecules lmnopqrstuvwxyz
#34: Protein | Mass: 29245.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0S7T8 |
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#35: Protein | Mass: 29800.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0S1A6 |
#36: Protein | Mass: 23679.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0S1Z0 |
#37: Protein | Mass: 27490.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0RY43 |
#38: Protein | Mass: 23084.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0S8C4 |
#39: Protein | Mass: 23102.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0RY45 |
#40: Protein | Mass: 22029.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0S0Z4 |
#41: Protein | Mass: 16912.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0RZM9 |
#42: Protein | Mass: 16071.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0SFL1 |
#43: Protein | Mass: 15962.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0SBR7 |
#44: Protein | Mass: 18698.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0SF00 |
#45: Protein | Mass: 14905.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0SHI0 |
#46: Protein | Mass: 15934.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0RY17 |
#47: Protein | Mass: 15535.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P0CU28 |
#48: Protein | Mass: 7741.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0S9M9 |
-RNA chain , 2 types, 2 molecules 12
#50: RNA chain | Mass: 827801.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
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#51: RNA chain | Mass: 87992.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
-Non-polymers , 1 types, 1 molecules ![](data/chem/img/ZN.gif)
#52: Chemical | ChemComp-ZN / |
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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: The 90S Pre-ribosomne / Type: COMPLEX / Entity ID: #1-#51 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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 | Electron dose: 2.4 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 231121 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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