[English] 日本語

- EMDB-30585: Cryo-EM structure of 90S preribosome with inactive Utp24 (state F1) -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-30585 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of 90S preribosome with inactive Utp24 (state F1) | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | ribosome assembly / 90S to pre-40S transition / cryo-EM / Dhr1 / Utp24 / RIBOSOME | |||||||||
Function / homology | ![]() regulation of ribosomal protein gene transcription by RNA polymerase II / Noc4p-Nop14p complex / box H/ACA snoRNA binding / RNA fragment catabolic process / rRNA 2'-O-methylation / CURI complex / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / Mpp10 complex ...regulation of ribosomal protein gene transcription by RNA polymerase II / Noc4p-Nop14p complex / box H/ACA snoRNA binding / RNA fragment catabolic process / rRNA 2'-O-methylation / CURI complex / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / rRNA modification / box C/D sno(s)RNA binding / regulation of rRNA processing / septum digestion after cytokinesis / histone H2AQ104 methyltransferase activity / snRNA binding / RNA folding chaperone / box C/D sno(s)RNA 3'-end processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rDNA heterochromatin / 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 / box C/D methylation guide snoRNP complex / U4/U6 snRNP / positive regulation of rRNA processing / tRNA export from nucleus / single-stranded telomeric DNA binding / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / Negative regulators of DDX58/IFIH1 signaling / SUMOylation of RNA binding proteins / U4 snRNA binding / protein localization to nucleolus / O-methyltransferase activity / 90S preribosome assembly / mTORC1-mediated signalling / rRNA methylation / Protein hydroxylation / U4 snRNP / poly(U) RNA binding / U3 snoRNA binding / 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 / snoRNA binding / preribosome, small subunit precursor / establishment of cell polarity / Major pathway of rRNA processing in the nucleolus and cytosol / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / SRP-dependent cotranslational protein targeting to membrane / nucleolar large rRNA transcription by RNA polymerase I / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / Ub-specific processing proteases / ribosomal subunit export from nucleus / RNA processing / regulation of translational fidelity / 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 / RNA endonuclease activity / Transferases; Transferring one-carbon groups; Methyltransferases / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / spliceosomal complex / translational initiation / small-subunit processome / enzyme activator activity / helicase activity / mRNA splicing, via spliceosome / maintenance of translational fidelity / rRNA processing / peroxisome / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic translation / RNA helicase activity / rRNA binding / RNA helicase / structural constituent of ribosome / ribosome / translation / mRNA binding / GTPase activity / GTP binding / nucleolus Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.0 Å | |||||||||
![]() | Du Y / Zhang J | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Cryo-EM structure of 90S preribosome with inactive Utp24 (state F1) Authors: Ye K | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 15.7 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 92.1 KB 92.1 KB | Display Display | ![]() |
Images | ![]() | 59.6 KB | ||
Filedesc metadata | ![]() | 25.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 400.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 400.5 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 8.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7d5tMC ![]() 7d4iC ![]() 7d5sC ![]() 7d63C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.328 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
+Entire : 90S pre-ribosome (state F1)
+Supramolecule #1: 90S pre-ribosome (state F1)
+Macromolecule #1: U3 snoRNA
+Macromolecule #2: 5' ETS
+Macromolecule #3: 18S rRNA
+Macromolecule #4: 40S ribosomal protein S1-A
+Macromolecule #5: 40S ribosomal protein S4-A
+Macromolecule #6: 40S ribosomal protein S5
+Macromolecule #7: 40S ribosomal protein S6-A
+Macromolecule #8: 40S ribosomal protein S7-A
+Macromolecule #9: 40S ribosomal protein S8-A
+Macromolecule #10: 40S ribosomal protein S9-A
+Macromolecule #11: 40S ribosomal protein S11-A
+Macromolecule #12: 40S ribosomal protein S13
+Macromolecule #13: 40S ribosomal protein S14-A
+Macromolecule #14: 40S ribosomal protein S16-A
+Macromolecule #15: 40S ribosomal protein S22-B
+Macromolecule #16: 40S ribosomal protein S23-A
+Macromolecule #17: 40S ribosomal protein S24-A
+Macromolecule #18: 40S ribosomal protein S27-A
+Macromolecule #19: 40S ribosomal protein S28-A
+Macromolecule #20: rRNA 2'-O-methyltransferase fibrillarin
+Macromolecule #21: Nucleolar protein 56
+Macromolecule #22: Nucleolar protein 58
+Macromolecule #23: Ribosomal RNA-processing protein 9
+Macromolecule #24: 13 kDa ribonucleoprotein-associated protein
+Macromolecule #25: U3 small nucleolar RNA-associated protein 5
+Macromolecule #26: U3 small nucleolar RNA-associated protein 10
+Macromolecule #27: NET1-associated nuclear protein 1
+Macromolecule #28: Periodic tryptophan protein 2
+Macromolecule #29: U3 small nucleolar RNA-associated protein 12
+Macromolecule #30: U3 small nucleolar RNA-associated protein 13
+Macromolecule #31: U3 small nucleolar RNA-associated protein 18
+Macromolecule #32: U3 small nucleolar RNA-associated protein 21
+Macromolecule #33: U3 small nucleolar RNA-associated protein 6
+Macromolecule #34: U3 small nucleolar RNA-associated protein 7
+Macromolecule #35: U3 small nucleolar RNA-associated protein 11
+Macromolecule #36: U3 small nucleolar RNA-associated protein MPP10
+Macromolecule #37: U3 small nucleolar ribonucleoprotein protein IMP3
+Macromolecule #38: U3 small nucleolar ribonucleoprotein protein IMP4
+Macromolecule #39: Something about silencing protein 10
+Macromolecule #40: Protein SOF1
+Macromolecule #41: rRNA-processing protein FCF2
+Macromolecule #42: rRNA-processing protein FCF1
+Macromolecule #43: rRNA biogenesis protein RRP5
+Macromolecule #44: U3 small nucleolar RNA-associated protein 22
+Macromolecule #45: Ribosomal RNA-processing protein 7
+Macromolecule #46: Ribosome biogenesis protein BMS1
+Macromolecule #47: RNA 3'-terminal phosphate cyclase-like protein
+Macromolecule #48: Nucleolar complex protein 14
+Macromolecule #49: U3 small nucleolar RNA-associated protein 20
+Macromolecule #50: U3 small nucleolar RNA-associated protein 14
+Macromolecule #51: Pno1
+Macromolecule #52: Probable ATP-dependent RNA helicase DHR1
+Macromolecule #53: Unassigned peptides 1
+Macromolecule #54: ZINC ION
+Macromolecule #55: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #56: MAGNESIUM ION
+Macromolecule #57: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 2.0 mg/mL | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.4 Component:
| |||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 1 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 50 sec. | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Number grids imaged: 10 / Number real images: 18538 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |