+Open data
-Basic information
Entry | Database: PDB / ID: 5wlc | ||||||||||||||||||
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Title | The complete structure of the small subunit processome | ||||||||||||||||||
Components |
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Keywords | RIBOSOME / Ribosome assembly | ||||||||||||||||||
Function / homology | Function and homology information rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / mRNA modification / Noc4p-Nop14p complex / tRNA acetylation / box H/ACA snoRNA binding / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / t-UTP complex / RNA fragment catabolic process ...rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / mRNA modification / Noc4p-Nop14p complex / tRNA acetylation / box H/ACA snoRNA binding / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / t-UTP complex / RNA fragment catabolic process / CURI complex / UTP-C complex / rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA binding / histone H2AQ104 methyltransferase activity / nuclear microtubule / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / rRNA (pseudouridine) methyltransferase activity / regulation of rRNA processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA modification / septum digestion after cytokinesis / snRNA binding / positive regulation of RNA binding / SUMOylation of RNA binding proteins / box C/D sno(s)RNA 3'-end processing / tRNA export from nucleus / regulation of transcription by RNA polymerase I / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rDNA heterochromatin / rRNA methyltransferase activity / positive regulation of rRNA processing / box C/D methylation guide snoRNP complex / U4/U6 snRNP / rRNA base methylation / single-stranded telomeric DNA binding / rRNA primary transcript binding / 90S preribosome assembly / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / U4 snRNA binding / protein localization to nucleolus / O-methyltransferase activity / U4 snRNP / mTORC1-mediated signalling / rRNA methylation / poly(U) RNA binding / U3 snoRNA binding / : / poly(A)+ mRNA export from nucleus / 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 / precatalytic spliceosome / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / snoRNA binding / spliceosomal complex assembly / establishment of cell polarity / positive regulation of transcription by RNA polymerase I / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / nucleolar large rRNA transcription by RNA polymerase I / 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 / enzyme activator activity / proteasome assembly / 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) / RNA processing / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / U4/U6 x U5 tri-snRNP complex / RNA endonuclease activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Transferases; Transferring one-carbon groups; Methyltransferases / nuclear periphery / small-subunit processome / spliceosomal complex / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / mRNA splicing, via spliceosome / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / unfolded protein binding / ribosome biogenesis / cytoplasmic translation / small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / rRNA binding Similarity search - Function | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae BY4741 (yeast) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||||||||
Authors | Barandun, J. / Chaker-Margot, M. / Hunziker, M. / Klinge, S. | ||||||||||||||||||
Funding support | United States, European Union, Switzerland, Canada, France, 5items
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Citation | Journal: Nat Struct Mol Biol / Year: 2017 Title: The complete structure of the small-subunit processome. Authors: Jonas Barandun / Malik Chaker-Margot / Mirjam Hunziker / Kelly R Molloy / Brian T Chait / Sebastian Klinge / Abstract: The small-subunit processome represents the earliest stable precursor of the eukaryotic small ribosomal subunit. Here we present the cryo-EM structure of the Saccharomyces cerevisiae small-subunit ...The small-subunit processome represents the earliest stable precursor of the eukaryotic small ribosomal subunit. Here we present the cryo-EM structure of the Saccharomyces cerevisiae small-subunit processome at an overall resolution of 3.8 Å, which provides an essentially complete near-atomic model of this assembly. In this nucleolar superstructure, 51 ribosome-assembly factors and two RNAs encapsulate the 18S rRNA precursor and 15 ribosomal proteins in a state that precedes pre-rRNA cleavage at site A1. Extended flexible proteins are employed to connect distant sites in this particle. Molecular mimicry and steric hindrance, as well as protein- and RNA-mediated RNA remodeling, are used in a concerted fashion to prevent the premature formation of the central pseudoknot and its surrounding elements within the small ribosomal subunit. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5wlc.cif.gz | 4.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5wlc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5wlc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/5wlc ftp://data.pdbj.org/pub/pdb/validation_reports/wl/5wlc | HTTPS FTP |
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-Related structure data
Related structure data | 8859MC 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
-RNA chain , 3 types, 3 molecules L0L1L2
#1: RNA chain | Mass: 225543.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: GenBank: 1262303 |
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#2: RNA chain | Mass: 582052.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: GenBank: 874346701 |
#3: RNA chain | Mass: 106503.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: GenBank: 176452 |
+Protein , 63 types, 67 molecules L3L4L5L6L7L8L9LCLDLELFLGLHLILJLKLLLMLNLOLPLQLRLSLTLULVLWLXLY...
-Non-polymers , 1 types, 1 molecules
#67: 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 |
-Sample preparation
Component | Name: Small subunit processome / Type: COMPLEX / Entity ID: #1-#66 / Source: NATURAL | ||||||||||||||||||||||||||||||
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Molecular weight | Units: MEGADALTONS / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae BY4741 (yeast) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.7 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Details: 50 mA / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Ted Pella Inc. | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-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 FIELDBright-field microscopy / Nominal magnification: 22500 X / Nominal defocus max: 2600 nm / Nominal defocus min: 600 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 0.25 sec. / Electron dose: 1.56 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 10029 |
Image scans | Movie frames/image: 32 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 772120 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 284213 / Num. of class averages: 2 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 338.9 / Protocol: OTHER / Space: REAL |