|Entry||Database: EMDB / ID: 3890|
|Title||State D (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes|
|Map data||State D (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||27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / Nucleolar complex-associated protein 3 / Noc2p-Noc3p complex / AdoMet-dependent rRNA methyltransferase, Spb1 / ec:184.108.40.2060: / RNA (C5-cytosine) methyltransferase, NOP2 / Ribosomal RNA methyltransferase Spb1, domain of unknown function DUF3381 / Nucleolar complex-associated protein 3, N-terminal / Ribosomal RNA methyltransferase, Spb1, C-terminal / Ribosome biogenesis factor, NIP7 ...27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / Nucleolar complex-associated protein 3 / Noc2p-Noc3p complex / AdoMet-dependent rRNA methyltransferase, Spb1 / ec:220.127.116.110: / RNA (C5-cytosine) methyltransferase, NOP2 / Ribosomal RNA methyltransferase Spb1, domain of unknown function DUF3381 / Nucleolar complex-associated protein 3, N-terminal / Ribosomal RNA methyltransferase, Spb1, C-terminal / Ribosome biogenesis factor, NIP7 / rRNA (guanine) methyltransferase activity / Domain of unknown function (DUF3381) / Spb1 C-terminal domain / Nucleolar complex-associated protein / CCAAT-binding factor / Ribosome biogenesis factor NIP7-like / WD repeat WDR12/Ytm1 / Ribosomal RNA large subunit methyltransferase E / CBF/Mak21 family / rRNA (cytosine-C5-)-methyltransferase activity / rRNA (uridine-2'-O-)-methyltransferase activity / Guanine nucleotide-binding protein-like 3, N-terminal domain / Nop2p / Uncharacterised protein family UPF0642 / Ribosomal RNA small subunit methyltransferase F, N-terminal / Uncharacterised protein family (UPF0113) / Eukaryotic rRNA processing / GTP-binding protein, orthogonal bundle domain superfamily / Mak16 protein / Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p, conserved site / cell cycle DNA replication / NOL1/NOP2/sun family signature. / snoRNA release from pre-rRNA / Ribosome biogenesis protein Nop16 / maturation of 5.8S rRNA / Ribosome biogenesis protein BRX1 / GNL3L/Grn1 putative GTPase / Protein of unknown function (DUF2423) / WDR74/Nsa1 / Ribosome assembly factor Mrt4 / Nucleolar, Nop52 / WD repeat BOP1/Erb1 / BOP1, N-terminal domain / Nucleolar GTP-binding protein 1 / NOG, C-terminal / Nucleolar GTP-binding protein 1, Rossman-fold domain / Domain of unknown function DUF4217 / nuclear division / NLE / Pescadillo / Eukaryotic rRNA processing protein EBP2 / Ribosome biogenesis protein 15, RNA recognition motif / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Mak16 protein C-terminal region / Ribosome biogenesis protein Nop16 / regulation of rRNA processing / N-terminal domain of 16S rRNA methyltransferase RsmF / RNA (C5-cytosine) methyltransferase / BOP1NT (NUC169) domain / SAM-dependent methyltransferase RsmB/NOP2-type / SAM-dependent MTase RsmB/NOP-type domain profile. / Domain of unknown function (DUF4217) / Nucleolar protein,Nop52 / PeBoW complex / NOGCT (NUC087) domain / Nucleolar GTP-binding protein 1 (NOG1) / Pescadillo N-terminus / rRNA primary transcript binding / NLE (NUC135) domain / 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 / OBG-type guanine nucleotide-binding (G) domain profile. / 16S rRNA methyltransferase RsmB/F / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PUA domain superfamily / nuclear pre-replicative complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / actomyosin contractile ring assembly / PUA domain / PUA domain profile. / eIF-6 family / Brix domain / mature ribosome assembly / regulation of cell division / rRNA base methylation / RNA-dependent ATPase activity / ribosomal subunit export from nucleus / Ribosomal L28e/Mak16 / chromosome organization / BRCT domain, a BRCA1 C-terminus domain / nuclear-transcribed mRNA catabolic process / pre-mRNA 5'-splice site binding / 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|
Function and homology information
|Source||Saccharomyces cerevisiae / / yeast /|
|Method||Cryo EM / single particle reconstruction / 4.2 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: 6em5|
SummaryFull reportAbout validation report
|Date||Deposition: Sep 29, 2017 / Header (metadata) release: Nov 15, 2017 / Map release: Dec 27, 2017 / Last update: Dec 27, 2017|
Downloads & links
|File||emd_3890.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: 34453|
|3D reconstruction||Algorithm: FOURIER SPACE / Software: RELION / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF|
|FSC plot (resolution assessment)|
-Atomic model buiding
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
-Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- All the functionalities will be ported from the levgacy version.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi