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- PDB-7d5s: Cryo-EM structure of 90S preribosome with inactive Utp24 (state A2) -
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Open data
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Basic information
Entry | Database: PDB / ID: 7d5s | |||||||||
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Title | Cryo-EM structure of 90S preribosome with inactive Utp24 (state A2) | |||||||||
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![]() | RIBOSOME / ribosome assembly / 90S to pre-40S transition / cryo-EM / Dhr1 / Utp24 | |||||||||
Function / homology | ![]() box H/ACA snoRNA binding / 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 / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / UTP-C complex ...box H/ACA snoRNA binding / 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 / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / UTP-C complex / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / rRNA modification / nuclear microtubule / regulation of rRNA processing / histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA binding / snRNA binding / positive regulation of RNA binding / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / septum digestion after cytokinesis / box C/D sno(s)RNA 3'-end processing / tRNA export from nucleus / 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) / regulation of transcription by RNA polymerase I / positive regulation of rRNA processing / U4/U6 snRNP / single-stranded telomeric DNA binding / rRNA primary transcript binding / 90S preribosome assembly / rRNA base methylation / O-methyltransferase activity / SUMOylation of RNA binding proteins / sno(s)RNA-containing ribonucleoprotein complex / protein localization to nucleolus / U4 snRNA binding / poly(U) RNA binding / box C/D methylation guide snoRNP complex / Protein hydroxylation / rRNA methylation / U4 snRNP / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / U3 snoRNA binding / 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 / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / 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 / regulation of translational fidelity / RNA processing / ribosomal subunit export from nucleus / Cajal body / 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 / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / spliceosomal complex / mRNA splicing, via spliceosome / rRNA processing / 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 / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / cell cycle / GTPase activity / mRNA binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
![]() | Du, Y. / Zhang, J. / An, W. / Ye, K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of 90S preribosome with inactive Utp24 (state A2) Authors: Ye, K. | |||||||||
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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Download
PDBx/mmCIF format | ![]() | 4.1 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 478.9 KB | Display | |
Data in CIF | ![]() | 770.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 30584MC ![]() 7d4iC ![]() 7d5tC ![]() 7d63C 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
+RNA chain , 3 types, 3 molecules 3A5ASA
+40S ribosomal protein ... , 9 types, 9 molecules SGSKSNSOSPSRSTSYSd
+Protein , 15 types, 18 molecules 3B3C3G3HAGB15B5H5IRCRDRGRHRKRSRTRWX1
+Nucleolar protein ... , 2 types, 2 molecules 3D3E
+Ribosomal RNA-processing protein ... , 2 types, 2 molecules 3FRF
+U3 small nucleolar RNA-associated protein ... , 16 types, 16 molecules A4A5A8A9AEAFB2B3B8BEB65C5D5ERERQ
+U3 small nucleolar ribonucleoprotein protein ... , 2 types, 2 molecules 5F5G
+RRNA-processing protein ... , 2 types, 2 molecules 5J5K
+Ribosome biogenesis protein ... , 2 types, 2 molecules RIRJ
+Nucleolar complex protein ... , 2 types, 2 molecules RNRO
+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)
+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-ribosome (state A2) / Type: COMPLEX / Entity ID: #1-#55 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 5 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: ![]() ![]() | |||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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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 / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 10 / Num. of real images: 18538 |
Image scans | Movie frames/image: 32 / Used frames/image: 1-32 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 913852 | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40111 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6LQU Accession code: 6LQU / Source name: PDB / Type: experimental model |