- EMDB-8473: Architecture of the yeast small subunit processome -
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Basic information
Entry
Database: EMDB / ID: EMD-8473
Title
Architecture of the yeast small subunit processome
Map data
Sample
Small subunit processome
(nucleic-acidNucleic acid) x 6
rpS6_ES6
rpS4_ES4
rpS5_US7
rpS7_eS7
rpS8_eS8
rpS9_uS4
rpS16_uS9
rpS11_uS17
rpS22_uS8
rpS24_eS24
rpS28_eS28
Utp4
UtpA_CTD1
UtpA_CTD2
(Beta-propeller ...) x 3
Utp17
Utp1
Utp6
Utp12
Utp13
Utp18
Utp21
Enp2
UtpA_CTD4
(Kre33) x 2
Imp3
Nop56
Nop58
(Nop1) x 2
Snu13NHP2L1
Ribosomal RNA-processing protein 9
RNA 3'-terminal phosphate cyclase-like protein
Bms1,Ribosome biogenesis protein BMS1,Bms1
Ribosomal RNA small subunit methyltransferase NEP1
Utp24
Imp4
Utp30
Unassigned KH domain
Utp20
(Repeat protein ...) x 2
40S ribosomal protein S23-ARibosome
Unassigned protein helices
Function / homology
Function and homology information
Pwp2p-containing subcomplex of 90S preribosome / rRNA small subunit pseudouridine methyltransferase Nep1 / rRNA (pseudouridine) methyltransferase activity / rRNA 2'-O-methylation / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of RNA binding / nuclear microtubule / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D RNP complex ...Pwp2p-containing subcomplex of 90S preribosome / rRNA small subunit pseudouridine methyltransferase Nep1 / rRNA (pseudouridine) methyltransferase activity / rRNA 2'-O-methylation / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of RNA binding / nuclear microtubule / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D RNP complex / rRNA base methylation / U4 snRNA binding / U3 snoRNA binding / rRNA export from nucleus / precatalytic spliceosome / 90S preribosome / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / rRNA methylation / snoRNA binding / 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) / maturation of SSU-rRNA / regulation of translational fidelity / U4/U6 x U5 tri-snRNP complex / small-subunit processome / ribosomal small subunit biogenesis / nuclear periphery / maturation of LSU-rRNA / endoribonuclease activity / maintenance of translational fidelity / positive regulation of translational fidelity / enzyme activator activity / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA processing / mRNA splicing, via spliceosome / cytoplasmic translation / ribosome biogenesis / cytosolic small ribosomal subunit / small ribosomal subunit / ribosome / rRNA binding / structural constituent of ribosome / translation / ATPase / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Ribosomal protein S4/S9, eukaryotic/archaeal / AARP2CN / Ribosomal protein S5/S7 / RNA 3'-terminal phosphate cyclase / Small-subunit processome, Utp21 / Quinoprotein alcohol dehydrogenase-like superfamily / Nucleic acid-binding, OB-fold / Ribosomal protein L23/L15e core domain superfamily / RNA 3'-terminal phosphate cyclase, insert domain / Ribosomal protein S28e ...Ribosomal protein S4/S9, eukaryotic/archaeal / AARP2CN / Ribosomal protein S5/S7 / RNA 3'-terminal phosphate cyclase / Small-subunit processome, Utp21 / Quinoprotein alcohol dehydrogenase-like superfamily / Nucleic acid-binding, OB-fold / Ribosomal protein L23/L15e core domain superfamily / RNA 3'-terminal phosphate cyclase, insert domain / Ribosomal protein S28e / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein S17/S11 / Ribosomal protein S7e / Ribosomal protein S12/S23 / RNA-binding S4 domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosome biogenesis protein BMS1/TSR1, C-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae conserved site / ATPase, AAA-type, core / H/ACA ribonucleoprotein complex, subunit Nhp2, eukaryote / Ribosomal protein S8 / Ribosomal protein S24e / Ribosomal protein S4/S9, N-terminal / WD40 repeat / Ribosomal protein S6e / Ribosomal protein S8e / Ribosomal protein S4e / Ribosomal protein S9 / RNA 3'-terminal phosphate cyclase type 2 / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / RNA 3'-terminal phosphate cyclase, insert domain superfamily / Alpha/beta knot methyltransferases / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S28e conserved site / RNA-binding S4 domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / Ribosome biogenesis protein Bms1, N-terminal / Ribosomal protein S4e, central domain superfamily / Ribosomal RNA-processing protein Rrp9-like / Ribosome biogenesis protein Bms1/Tsr1 / Ribosomal protein S4, KOW domain / tRNA (guanine-N1-)-methyltransferase, N-terminal / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal S24e conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / WD40 repeat, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S9, conserved site / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S7, conserved site / RNA 3'-terminal phosphate cyclase-like, conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein S7 domain / Anaphase-promoting complex subunit 4, WD40 domain / KOW
40S ribosomal protein S5 / Ribosome biogenesis protein BMS1 / RNA 3'-terminal phosphate cyclase-like protein / Ribosomal RNA-processing protein 9 / Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar RNA-associated protein 21 / 13 kDa ribonucleoprotein-associated protein / 40S ribosomal protein S7-A / 40S ribosomal protein S11-A / 40S ribosomal protein S16-A ...40S ribosomal protein S5 / Ribosome biogenesis protein BMS1 / RNA 3'-terminal phosphate cyclase-like protein / Ribosomal RNA-processing protein 9 / Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar RNA-associated protein 21 / 13 kDa ribonucleoprotein-associated protein / 40S ribosomal protein S7-A / 40S ribosomal protein S11-A / 40S ribosomal protein S16-A / 40S ribosomal protein S8-A / 40S ribosomal protein S6-A / 40S ribosomal protein S4-A / 40S ribosomal protein S24-A / 40S ribosomal protein S23-A / 40S ribosomal protein S22-A / 40S ribosomal protein S9-A / 40S ribosomal protein S28-A
Journal: Science / Year: 2017 Title: Architecture of the yeast small subunit processome. Authors: Malik Chaker-Margot / Jonas Barandun / Mirjam Hunziker / Sebastian Klinge / Abstract: The small subunit (SSU) processome, a large ribonucleoprotein particle, organizes the assembly of the eukaryotic small ribosomal subunit by coordinating the folding, cleavage, and modification of ...The small subunit (SSU) processome, a large ribonucleoprotein particle, organizes the assembly of the eukaryotic small ribosomal subunit by coordinating the folding, cleavage, and modification of nascent pre-ribosomal RNA (rRNA). Here, we present the cryo-electron microscopy structure of the yeast SSU processome at 5.1-angstrom resolution. The structure reveals how large ribosome biogenesis complexes assist the 5' external transcribed spacer and U3 small nucleolar RNA in providing an intertwined RNA-protein assembly platform for the separate maturation of 18S rRNA domains. The strategic placement of a molecular motor at the center of the particle further suggests a mechanism for mediating conformational changes within this giant particle. This study provides a structural framework for a mechanistic understanding of eukaryotic ribosome assembly in the model organism Saccharomyces cerevisiae.
Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 % Details: Incubated 10 seconds on the grid before blotting (blot time 2.0 seconds, blot force 0) and freezing..
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Electron microscopy imaging
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
Imaging
Microscope: FEI TITAN KRIOS
Electron gun
Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.56 e/Å2 / Illumination mode: FLOOD BEAM
Lens
Magnification: 22500. X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 600.0 - 2600.0 nm
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