6em3: Difference between revisions

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-'''Unreleased structure'''
-The entry 6em3 is ON HOLD
+==State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes==
+<SX load='6em3' size='340' side='right' viewer='molstar' caption='[[6em3]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6em3]] is a 33 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_(strain_atcc_204508_/_s288c) Saccharomyces cerevisiae (strain atcc 204508 / s288c)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EM3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6EM3 FirstGlance]. <br>
+</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6em3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6em3 OCA], [http://pdbe.org/6em3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6em3 RCSB], [http://www.ebi.ac.uk/pdbsum/6em3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6em3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/ERB1_YEAST ERB1_YEAST]] Component of the NOP7 complex, which is required for maturation of the 25S and 5.8S ribosomal RNAs and formation of the 60S ribosome.[HAMAP-Rule:MF_03027]<ref>PMID:11522832</ref> <ref>PMID:18448671</ref>  [[http://www.uniprot.org/uniprot/EBP2_YEAST EBP2_YEAST]] Required for the processing of the 27S pre-rRNA. Probably involved in the step of the processing of the 27 SA precursor into the 27 SB intermediate.<ref>PMID:10849420</ref> <ref>PMID:10947841</ref>  [[http://www.uniprot.org/uniprot/RPF1_YEAST RPF1_YEAST]] Essential protein. Required for biogenesis of the 60S ribosomal subunit.<ref>PMID:11864606</ref> <ref>PMID:12702244</ref>  [[http://www.uniprot.org/uniprot/NOP15_YEAST NOP15_YEAST]] Involved in the biogenesis of the 60S ribosomal subunit. Required for pre-rRNA processing and cytokinesis. Associates with the precursors of the 25S and 5.8S rRNAs.<ref>PMID:11583614</ref> <ref>PMID:14657029</ref>  [[http://www.uniprot.org/uniprot/RL37A_YEAST RL37A_YEAST]] Binds to the 23S rRNA (By similarity). [[http://www.uniprot.org/uniprot/PESC_YEAST PESC_YEAST]] Component of the NOP7 complex, which is required for maturation of the 25S and 5.8S ribosomal RNAs and formation of the 60S ribosome.[HAMAP-Rule:MF_03028]<ref>PMID:11911362</ref> <ref>PMID:12022229</ref> <ref>PMID:12110181</ref> <ref>PMID:18448671</ref>  [[http://www.uniprot.org/uniprot/BRX1_YEAST BRX1_YEAST]] Required for biogenesis of the 60S ribosomal subunit.<ref>PMID:11843177</ref>  [[http://www.uniprot.org/uniprot/HAS1_YEAST HAS1_YEAST]] ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.<ref>PMID:15049817</ref> <ref>PMID:15242642</ref> <ref>PMID:15718299</ref>  [[http://www.uniprot.org/uniprot/CIC1_YEAST CIC1_YEAST]] An adapter protein that specifically links the 26S proteasome to its substrate CDC4 which is one of the substrate recognition subunits of the SCF E3 ubiquitin ligase complex. Required for turnover of cell cycle regulatory proteins CDC4 and GRR1. Required for synthesis and nuclear export of 60S ribosomal subunits. Required for vegetative growth.<ref>PMID:11500370</ref> <ref>PMID:14623999</ref>  [[http://www.uniprot.org/uniprot/MAK16_YEAST MAK16_YEAST]] Its role might be as part of the apparatus concerned with the nuclear events of the cell cycle.<ref>PMID:3045810</ref>  [[http://www.uniprot.org/uniprot/RL4A_YEAST RL4A_YEAST]] Participates in the regulation of the accumulation of its own mRNA.<ref>PMID:2065661</ref>  [[http://www.uniprot.org/uniprot/RL36B_YEAST RL36B_YEAST]] Component of the ribosome, a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. The small ribosomal subunit (SSU) binds messenger RNAs (mRNAs) and translates the encoded message by selecting cognate aminoacyl-transfer RNA (tRNA) molecules. The large subunit (LSU) contains the ribosomal catalytic site termed the peptidyl transferase center (PTC), which catalyzes the formation of peptide bonds, thereby polymerizing the amino acids delivered by tRNAs into a polypeptide chain. The nascent polypeptides leave the ribosome through a tunnel in the LSU and interact with protein factors that function in enzymatic processing, targeting, and the membrane insertion of nascent chains at the exit of the ribosomal tunnel.<ref>PMID:22096102</ref>  [[http://www.uniprot.org/uniprot/NOP16_YEAST NOP16_YEAST]] Involved in the biogenesis of the 60S ribosomal subunit.<ref>PMID:11583614</ref>  [[http://www.uniprot.org/uniprot/RRP1_YEAST RRP1_YEAST]] Required for 27S rRNA processing to 25S and 5.8S. [[http://www.uniprot.org/uniprot/RLP7_YEAST RLP7_YEAST]] Involved in the biogenesis of the 60S ribosomal subunit. May act as a specificity factor that binds precursor rRNAs and tethers the enzymes that carry out the early 5' to 3' exonucleolytic reactions that generate the mature rRNAs.<ref>PMID:11087857</ref>  [[http://www.uniprot.org/uniprot/NSA1_YEAST NSA1_YEAST]] Involved in the biogenesis of the 60S ribosomal subunit.<ref>PMID:16544271</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and approximately 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 A to 4.5 A 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.
-Authors:
+Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes.,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 Cell. 2017 Dec 14;171(7):1599-1610.e14. doi: 10.1016/j.cell.2017.11.039. PMID:29245012<ref>PMID:29245012</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6em3" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ribosome 3D structures|Ribosome 3D structures]]
+*[[Ribosome biogenesis protein|Ribosome biogenesis protein]]
+== References ==
+<references/>
+__TOC__
+</SX>
+[[Category: Large Structures]]
+[[Category: RNA helicase]]
+[[Category: Barrio-Garcia, C]]
+[[Category: Beckmann, R]]
+[[Category: Cheng, J]]
+[[Category: Hurt, E]]
+[[Category: Kater, L]]
+[[Category: Large subunit biogenesis nucleolus]]
+[[Category: Ribosome]]