|Entry||Database: EMDB / ID: 3893|
|Title||State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes|
|Map data||State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosmes|
|Sample||Large subunit biogenesis particle purified via Nsa1-TAP and Flag-Ytm1|
|Function/homology||Guanine nucleotide-binding protein-like 3, N-terminal domain / Uncharacterised protein family UPF0642 / Eukaryotic rRNA processing / Mak16 protein / snoRNA release from pre-rRNA / Ribosome biogenesis protein Nop16 / GTP-binding protein, orthogonal bundle domain superfamily / Ribosome biogenesis protein BRX1 / WDR74/Nsa1 / GNL3L/Grn1 putative GTPase ...Guanine nucleotide-binding protein-like 3, N-terminal domain / Uncharacterised protein family UPF0642 / Eukaryotic rRNA processing / Mak16 protein / snoRNA release from pre-rRNA / Ribosome biogenesis protein Nop16 / GTP-binding protein, orthogonal bundle domain superfamily / Ribosome biogenesis protein BRX1 / WDR74/Nsa1 / GNL3L/Grn1 putative GTPase / Protein of unknown function (DUF2423) / Ribosome assembly factor Mrt4 / Nucleolar, Nop52 / Nucleolar GTP-binding protein 1 / WD repeat BOP1/Erb1 / NOG, C-terminal / BOP1, N-terminal domain / Nucleolar GTP-binding protein 1, Rossman-fold domain / Domain of unknown function DUF4217 / nuclear division / Pescadillo / Eukaryotic rRNA processing protein EBP2 / Mak16 protein C-terminal region / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ribosome biogenesis protein 15, RNA recognition motif / Ribosome biogenesis protein Nop16 / BOP1NT (NUC169) domain / Nucleolar protein,Nop52 / Domain of unknown function (DUF4217) / PeBoW complex / NOGCT (NUC087) domain / Pescadillo N-terminus / Nucleolar GTP-binding protein 1 (NOG1) / rRNA primary transcript binding / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Brix domain / Brix domain profile. / Translation initiation factor IF6 / OBG-type guanine nucleotide-binding (G) domain profile. / OBG-type guanine nucleotide-binding (G) domain / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / actomyosin contractile ring assembly / eIF-6 family / Brix domain / mature ribosome assembly / regulation of cell division / RNA-dependent ATPase activity / ribosomal subunit export from nucleus / Ribosomal L28e/Mak16 / BRCT domain, a BRCA1 C-terminus domain / nuclear-transcribed mRNA catabolic process / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / GTP binding domain / Ribosomal L28e protein family / ATPase activator activity / ribosomal large subunit binding / preribosome, small subunit precursor / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / Ribosomal protein L13e, conserved site / preribosome, large subunit precursor / Ribosomal protein L13e signature. / TRASH domain / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L6e signature. / DEAD-box RNA helicase Q motif profile. / RNA helicase, DEAD-box type, Q motif / proteasome binding / 50S ribosome-binding GTPase / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Ribosomal protein L35Ae signature. / Ribosomal protein L35Ae, conserved site / RNA secondary structure unwinding / Ribosomal protein L36e signature. / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Formation of a pool of free 40S subunits / Ribosomal protein L7, eukaryotic / 60S ribosomal protein L6E / Ribosomal protein L30, N-terminal / Ribosomal protein L7A/L8 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Ribosomal protein L36e / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L35A / Ribosomal protein L14e domain / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein L18e signature. / Ribosomal protein L18e, conserved site / ribosomal large subunit export from nucleus / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L18e / Ribosomal protein L13e / ribosomal large subunit biogenesis / L13a-mediated translational silencing of Ceruloplasmin expression|
Function and homology information
|Source||Saccharomyces cerevisiae / / yeast /|
|Method||Cryo EM / single particle reconstruction / 3.6 Å resolution|
|Authors||Kater L / Thoms M / Barrio-Garcia C / Cheng J / Ismail S / Ahmed YL / Bange G / Kressler D / Berninghausen O / Sinning I / Hurt E / Beckmann R|
|Citation||Journal: Cell / Year: 2017|
Title: Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes.
Authors: Lukas Kater / Matthias Thoms / Clara Barrio-Garcia / Jingdong Cheng / Sherif Ismail / Yasar Luqman Ahmed / Gert Bange / Dieter Kressler / Otto Berninghausen / Irmgard Sinning / Ed Hurt / Roland Beckmann
Abstract: Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural ...Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural information, this process is poorly understood. Using cryo-EM, we solved structures of early 60S biogenesis intermediates at 3.3 Å to 4.5 Å resolution, thereby providing insights into their sequential folding and assembly pathway. Besides revealing distinct immature rRNA conformations, we map 25 assembly factors in six different assembly states. Notably, the Nsa1-Rrp1-Rpf1-Mak16 module stabilizes the solvent side of the 60S subunit, and the Erb1-Ytm1-Nop7 complex organizes and connects through Erb1's meandering N-terminal extension, eight assembly factors, three ribosomal proteins, and three 25S rRNA domains. Our structural snapshots reveal the order of integration and compaction of the six major 60S domains within early nucleolar 60S particles developing stepwise from the solvent side around the exit tunnel to the central protuberance.
Copyright: 2017 The Authors. Published by Elsevier Inc. All rights reserved.
|Validation Report||PDB-ID: 6em1|
SummaryFull reportAbout validation report
|Date||Deposition: Sep 29, 2017 / Header (metadata) release: Dec 20, 2017 / Map release: Dec 27, 2017 / Last update: Dec 27, 2017|
Downloads & links
|File||emd_3893.map.gz (map file in CCP4 format, 296353 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.084 Å|
CCP4 map header:
-Entire Large subunit biogenesis particle purified via Nsa1-TAP and Flag-Ytm1
|Entire||Name: Large subunit biogenesis particle purified via Nsa1-TAP and Flag-Ytm1|
Number of components: 1
-Component #1: protein, Large subunit biogenesis particle purified via Nsa1-TAP ...
|Protein||Name: Large subunit biogenesis particle purified via Nsa1-TAP and Flag-Ytm1|
Recombinant expression: No
|Source||Species: Saccharomyces cerevisiae / / yeast /|
|Specimen||Specimen state: particle / Method: Cryo EM|
|Sample solution||pH: 7.5|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE|
-Electron microscopy imaging
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: 27 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Cs: 2.7 mm / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of projections: 156937|
|3D reconstruction||Algorithm: FOURIER SPACE / Software: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF|
|FSC plot (resolution assessment)|
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