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- PDB-7d4i: Cryo-EM structure of 90S small ribosomal precursors complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7d4i | |||||||||
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Title | Cryo-EM structure of 90S small ribosomal precursors complex with the DEAH-box RNA helicase Dhr1 (State F) | |||||||||
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![]() | RIBOSOME / ribosome assembly / 90S to pre-40S transition / cryo-EM / Dhr1 / Utp24 | |||||||||
Function / homology | ![]() nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / mRNA decay by 3' to 5' exoribonuclease / nuclear polyadenylation-dependent CUT catabolic process ...nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / mRNA decay by 3' to 5' exoribonuclease / nuclear polyadenylation-dependent CUT catabolic process / regulatory ncRNA 3'-end processing / box H/ACA snoRNA binding / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / rRNA 2'-O-methylation / CUT catabolic process / exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / U1 snRNA 3'-end processing / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / CURI complex / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / nuclear exosome (RNase 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-transcribed mRNA catabolic process, non-stop decay / nuclear microtubule / poly(A)-dependent snoRNA 3'-end processing / regulation of rRNA processing / U4 snRNA 3'-end processing / histone H2AQ104 methyltransferase activity / : / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA binding / : / 3'-5' RNA helicase activity / snRNA binding / positive regulation of RNA binding / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone mRNA catabolic process / nuclear mRNA surveillance / septum digestion after cytokinesis / box C/D sno(s)RNA 3'-end processing / tRNA export from nucleus / rDNA heterochromatin / rRNA catabolic process / nonfunctional rRNA decay / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / 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 / poly(A) binding / U4/U6 snRNP / single-stranded telomeric DNA binding / rRNA primary transcript binding / 90S preribosome assembly / rRNA base methylation / Negative regulators of DDX58/IFIH1 signaling / O-methyltransferase activity / SUMOylation of RNA binding proteins / sno(s)RNA-containing ribonucleoprotein complex / protein localization to nucleolus / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / U4 snRNA binding / poly(U) RNA binding / box C/D methylation guide snoRNP complex / mTORC1-mediated signalling / Protein hydroxylation / RNA catabolic process / 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 / rRNA metabolic process / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / spliceosomal complex assembly / SRP-dependent cotranslational protein targeting to membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | |||||||||
![]() | Du, Y. / Zhang, J. / An, W. / Ye, K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of 90S small ribosomal precursors complex with Dhr1 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 | ![]() | 5.7 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 625.6 KB | Display | |
Data in CIF | ![]() | 1 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 30574MC ![]() 7d5sC ![]() 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 ... , 18 types, 18 molecules SCSFSGSHSISJSKSMSOSPSRSTSUSXSYSZScSd
+Protein , 18 types, 21 molecules 3B3C3G3HAGB15B5H5IRDRGRHRJRKRSRTRWRZR7M4M6
+Nucleolar protein ... , 2 types, 2 molecules 3D3E
+Ribosomal RNA-processing protein ... , 2 types, 2 molecules 3FRF
+U3 small nucleolar RNA-associated protein ... , 17 types, 17 molecules A4A5A8A9AEAFB2B3B8BEB65C5D5ERERPRQ
+U3 small nucleolar ribonucleoprotein protein ... , 2 types, 2 molecules 5F5G
+RRNA-processing protein ... , 2 types, 2 molecules 5J5K
+Nucleolar complex protein ... , 2 types, 2 molecules RNRO
+Unassigned peptides ... , 2 types, 2 molecules X1X2
+Exosome complex component ... , 9 types, 9 molecules R5R1R3R6R2M3R0r4C4
+Exosome complex exonuclease ... , 2 types, 2 molecules R4r6
+Non-polymers , 4 types, 5 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.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 F) / Type: COMPLEX / Entity ID: #1-#79 / 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 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 219545 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6LQS Accession code: 6LQS / Source name: PDB / Type: experimental model |