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Yorodumi- PDB-6rxv: Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaet... -
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-Basic information
Entry | Database: PDB / ID: 6rxv | ||||||
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Title | Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state B2 | ||||||
Components |
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Keywords | RIBOSOME / ribosome biogenesis / rRNA | ||||||
Function / homology | Function and homology information 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 / CURI complex / UTP-C complex / t-UTP complex / Mpp10 complex ...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 / CURI complex / UTP-C 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 / tRNA export from nucleus / rRNA base methylation / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / box C/D methylation guide snoRNP complex / U3 snoRNA binding / Cajal body / preribosome, small subunit precursor / snoRNA binding / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / 90S preribosome / RNA processing / 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) / 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 / cytosolic small ribosomal subunit / methylation / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / regulation of transcription by RNA polymerase II / nucleolus / GTP binding / RNA binding / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | Cheng, J. / Kellner, N. / Griesel, S. / Berninghausen, O. / Beckmann, R. / Hurt, E. | ||||||
Citation | Journal: Mol Cell / Year: 2019 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 6rxv.cif.gz | 5.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6rxv.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6rxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rxv_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6rxv_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6rxv_validation.xml.gz | 525.7 KB | Display | |
Data in CIF | 6rxv_validation.cif.gz | 895.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/6rxv ftp://data.pdbj.org/pub/pdb/validation_reports/rx/6rxv | HTTPS FTP |
-Related structure data
Related structure data | 10053MC 6rxtC 6rxuC 6rxxC 6rxyC 6rxzC 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
+Protein , 44 types, 49 molecules UAUBUCUDUFUGUJULUMUNUOUQURUUUXUZCACBCCCDCECFCGCHCICJCKCLCMCN...
-U3 small nucleolar RNA-associated protein ... , 2 types, 2 molecules UKUV
#8: Protein | Mass: 31379.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) References: UniProt: G0SF32 |
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#52: Protein | Mass: 131105.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) References: UniProt: G0S2E0 |
-40S ribosomal protein ... , 15 types, 15 molecules CaCbCcCdCeCfCgChCiCjCkCmCnCoCp
#34: Protein | Mass: 29245.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) 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) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) References: UniProt: G0S1A6 |
#36: Protein | Mass: 23679.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) References: UniProt: G0S1Z0 |
#37: Protein | Mass: 27490.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) References: UniProt: G0RY43 |
#38: Protein | Mass: 23084.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) References: UniProt: G0S8C4 |
#39: Protein | Mass: 23102.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) References: UniProt: G0RY45 |
#40: Protein | Mass: 22029.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) References: UniProt: G0S0Z4 |
#41: Protein | Mass: 16912.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) References: UniProt: G0RZM9 |
#42: Protein | Mass: 16071.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) References: UniProt: G0SFL1 |
#43: Protein | Mass: 15962.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) References: UniProt: G0SBR7 |
#44: Protein | Mass: 18698.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) References: UniProt: G0SF00 |
#45: Protein | Mass: 14905.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) References: UniProt: G0SHI0 |
#46: Protein | Mass: 15934.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) References: UniProt: G0RY17 |
#47: Protein | Mass: 15535.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) References: UniProt: P0CU28 |
#48: Protein | Mass: 7741.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) References: UniProt: G0S9M9 |
-RNA chain , 2 types, 2 molecules C1C2
#50: RNA chain | Mass: 758475.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) |
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#51: RNA chain | Mass: 73966.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) |
-Non-polymers , 3 types, 3 molecules
#64: Chemical | ChemComp-ZN / |
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#65: Chemical | ChemComp-GTP / |
#66: 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 |
-Sample preparation
Component | Name: 90S pre-ribosome, state B2 / Type: RIBOSOME / Entity ID: #1-#63 / Source: NATURAL |
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Source (natural) | Organism: Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 28 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48335 / Symmetry type: POINT |