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- PDB-6rxt: Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaet... -
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Basic information
Entry | Database: PDB / ID: 6rxt | ||||||
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Title | Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state A | ||||||
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![]() | RIBOSOME / ribosome biogenesis / rRNA | ||||||
Function / homology | ![]() tRNA wobble cytosine modification / rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA N-acetyltransferase activity / tRNA acetylation / Noc4p-Nop14p complex / t-UTP complex / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity ...tRNA wobble cytosine modification / rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA N-acetyltransferase activity / tRNA acetylation / Noc4p-Nop14p complex / 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 base methylation / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / box C/D methylation guide snoRNP complex / U3 snoRNA binding / preribosome, small subunit precursor / snoRNA binding / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / 90S preribosome / RNA processing / Cajal body / U4/U6 x U5 tri-snRNP complex / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RNA endonuclease activity / maturation of LSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / protein ubiquitination / structural constituent of ribosome / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / RNA binding / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å | ||||||
![]() | Cheng, J. / Kellner, N. / Griesel, S. / Berninghausen, O. / Beckmann, R. / Hurt, E. | ||||||
![]() | ![]() Title: Thermophile 90S Pre-ribosome Structures Reveal the Reverse Order of Co-transcriptional 18S rRNA Subdomain Integration. Authors: Jingdong Cheng / Jochen Baßler / Paulina Fischer / Benjamin Lau / Nikola Kellner / Ruth Kunze / Sabine Griesel / Martina Kallas / Otto Berninghausen / Daniela Strauss / Roland Beckmann / Ed Hurt / ![]() Abstract: Eukaryotic ribosome biogenesis involves RNA folding and processing that depend on assembly factors and small nucleolar RNAs (snoRNAs). The 90S (SSU-processome) is the earliest pre-ribosome ...Eukaryotic ribosome biogenesis involves RNA folding and processing that depend on assembly factors and small nucleolar RNAs (snoRNAs). The 90S (SSU-processome) is the earliest pre-ribosome structurally analyzed, which was suggested to assemble stepwise along the growing pre-rRNA from 5' > 3', but this directionality may not be accurate. Here, by analyzing the structure of a series of 90S assembly intermediates from Chaetomium thermophilum, we discover a reverse order of 18S rRNA subdomain incorporation. Large parts of the 18S rRNA 3' and central domains assemble first into the 90S before the 5' domain is integrated. This final incorporation depends on a contact between a heterotrimer Enp2-Bfr2-Lcp5 recruited to the flexible 5' domain and Kre33, which reconstitutes the Kre33-Enp-Brf2-Lcp5 module on the compacted 90S. Keeping the 5' domain temporarily segregated from the 90S scaffold could provide extra time to complete the multifaceted 5' domain folding, which depends on a distinct set of snoRNAs and processing factors. | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 3.9 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
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 | ![]() 10051MC ![]() 6rxuC ![]() 6rxvC ![]() 6rxxC ![]() 6rxyC ![]() 6rxzC 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 , 38 types, 43 molecules UAUBUCUDUFUGUJUKULUMUNUOUQURUUUXUZCACBCCCDCECFCGCHCICJCMCNCO...
-Putative U3 small nucleolar ... , 2 types, 2 molecules CKCL
#26: Protein | Mass: 34216.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#27: Protein | Mass: 86082.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-40S ribosomal protein ... , 10 types, 10 molecules CaCcCeCgChCiCjCmCnCp
#34: Protein | Mass: 29245.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#35: Protein | Mass: 23679.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#36: Protein | Mass: 23084.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#37: Protein | Mass: 22029.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#38: Protein | Mass: 16912.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#39: Protein | Mass: 16071.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#40: Protein | Mass: 15962.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#41: Protein | Mass: 14905.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#42: Protein | Mass: 15934.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#43: Protein | Mass: 7741.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-RNA chain , 2 types, 2 molecules C1C2
#45: RNA chain | Mass: 758475.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#46: RNA chain | Mass: 73966.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 3 types, 3 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
#53: Chemical | ChemComp-ZN / |
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#54: Chemical | ChemComp-GTP / |
#55: Chemical | ChemComp-MG / |
-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: 90S pre-ribosome, state A / Type: RIBOSOME / Entity ID: #1-#52 / 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: 28 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8415 / Symmetry type: POINT |