|Entry||Database: EMDB / ID: 8143|
|Title||nuclear ribo-nucleoprotein complex|
|Sample||nuclear ribo-nucleoprotein complex:|
|Function / homology||RNA 3'-terminal phosphate cyclase domain / tRNA (guanine-N1-)-methyltransferase, N-terminal / Ribosomal protein S7 domain / Ribosomal RNA assembly KRR1 / Anaphase-promoting complex subunit 4, WD40 domain / P-loop containing nucleoside triphosphate hydrolase / 40S ribosomal protein S1/3, eukaryotes / Possible tRNA binding domain / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L1/ribosomal biogenesis protein ...RNA 3'-terminal phosphate cyclase domain / tRNA (guanine-N1-)-methyltransferase, N-terminal / Ribosomal protein S7 domain / Ribosomal RNA assembly KRR1 / Anaphase-promoting complex subunit 4, WD40 domain / P-loop containing nucleoside triphosphate hydrolase / 40S ribosomal protein S1/3, eukaryotes / Possible tRNA binding domain / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S28e conserved site / Helix hairpin bin domain superfamily / Alpha/beta knot methyltransferases / Ribosomal protein S15P / PIN-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / TmcA/NAT10/Kre33 / RNA cytidine acetyltransferase NAT10 / Ribosomal protein S8 superfamily / Nop domain superfamily / Ribosomal protein L1-like / Ribosomal protein S4/S9 / RNA 3'-terminal phosphate cyclase, insert domain superfamily / Ribosomal protein S3Ae, conserved site / Ribosomal protein L2, domain 2 / WD40/YVTN repeat-like-containing domain superfamily / Armadillo-type fold / Ribosomal protein L1, 3-layer alpha/beta-sandwich / RNA 3'-terminal phosphate cyclase type 2 / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein L7Ae, archaea / Ribosomal protein L7Ae/L8/Nhp2 family / WD40 repeat, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / RNA 3'-terminal phosphate cyclase-like, conserved site / Fibrillarin, conserved site / U3 small nucleolar RNA-associated protein 10 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / WD40-repeat-containing domain superfamily / K Homology domain, type 1 superfamily / Ribosomal protein S9 signature. / AARP2CN (NUC121) domain / snoRNA binding domain, fibrillarin / EMG1/NEP1 methyltransferase / Utp21 specific WD40 associated putative domain / Brix domain / Fcf1 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / Helicase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / Ribosomal S13/S15 N-terminal domain / RS4NT (NUC023) domain / BP28CT (NUC211) domain / Ribosomal protein S24e / Domain of unknown function (DUF1726) / U3 small nucleolar RNA-associated protein 10 / Anaphase-promoting complex subunit 4 WD40 domain / GNAT acetyltransferase 2 / Possible tRNA binding domain / 40S ribosomal protein S4 C-terminus / Ribosomal_S17 N-terminal / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S11 signature. / S4 domain / Fibrillarin / Ribosomal protein S7 domain superfamily / Ribosomal protein S17 / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / rRNA-processing protein Fcf1, PIN domain / Ribosome biogenesis protein Bms1, N-terminal / Ribosomal protein S4e, central domain superfamily / ATPase family associated with various cellular activities (AAA) / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S7p/S5e / Ribosomal protein S15 / Ribosomal protein S9/S16 / Ribosomal protein S7e / WD domain, G-beta repeat / Ribosomal protein S8 / Ribosomal protein S11 / Ribosomal protein L1p/L10e family / Ribosomal family S4e / Ribosomal S3Ae family / Ribosomal protein S6e / RNA 3'-terminal phosphate cyclase|
Function and homology information
|Source||Chaetomium thermophilum (fungus)|
|Method||single particle reconstruction / cryo EM / 7.3 Å resolution|
|Authors||Kornprobst M / Turk M / Kellner N / Cheng J / Flemming D / Kos-Braun IC / Kos M / Thoms M / Berninghausen O / Beckmann R / Hurt E|
|Citation||Journal: Cell / Year: 2016|
Title: Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome.
Authors: Markus Kornprobst / Martin Turk / Nikola Kellner / Jingdong Cheng / Dirk Flemming / Isabelle Koš-Braun / Martin Koš / Matthias Thoms / Otto Berninghausen / Roland Beckmann / Ed Hurt
Abstract: The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that ...The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that associate with nascent pre-rRNA. We report the cryo-EM structure of the Chaetomium thermophilum 90S pre-ribosome, revealing how a network of biogenesis factors including 19 β-propellers and large α-solenoid proteins engulfs the pre-rRNA. Within the 90S pre-ribosome, we identify the UTP-A, UTP-B, Mpp10-Imp3-Imp4, Bms1-Rcl1, and U3 snoRNP modules, which are organized around 5'-ETS and partially folded 18S rRNA. The U3 snoRNP is strategically positioned at the center of the 90S particle to perform its multiple tasks during pre-rRNA folding and processing. The architecture of the elusive 90S pre-ribosome gives unprecedented structural insight into the early steps of pre-rRNA maturation. Nascent rRNA that is co-transcriptionally folded and given a particular shape by encapsulation within a dedicated mold-like structure is reminiscent of how polypeptides use chaperone chambers for their protein folding.
|Validation Report||PDB-ID: 5jpq|
SummaryFull reportAbout validation report
|Date||Deposition: Apr 5, 2016 / Header (metadata) release: Aug 3, 2016 / Map release: Aug 3, 2016 / Last update: Aug 3, 2016|
|Structure viewer||EM map: |
Downloads & links
|File||emd_8143.map.gz (map file in CCP4 format, 359662 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.068 Å|
CCP4 map header:
-Entire nuclear ribo-nucleoprotein complex
|Entire||Name: nuclear ribo-nucleoprotein complex / Number of components: 1|
-Component #1: protein, nuclear ribo-nucleoprotein complex
|Protein||Name: nuclear ribo-nucleoprotein complex / Recombinant expression: No|
|Source||Species: Chaetomium thermophilum (fungus)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||pH: 7.5|
|Vitrification||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: 2.66 e/Å2 / Illumination mode: SPOT SCAN|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 43116|
|3D reconstruction||Resolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF|
-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
+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
+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.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi