5wyk - Revision history

OCA at 22:30, 10 April 2020

OCA — Fri, 10 Apr 2020 22:30:27 GMT

←Older revision		Revision as of 22:30, 10 April 2020
Line 3:		Line 3:
	<SX load='5wyk' size='340' side='right' viewer='molstar' caption='[[5wyk]], [[Resolution\|resolution]] 4.50Å' scene=''>		<SX load='5wyk' size='340' side='right' viewer='molstar' caption='[[5wyk]], [[Resolution\|resolution]] 4.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wyk]] is a 58 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] and [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=5WYK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5WYK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wyk]] is a 58 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] and [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=5WYK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5WYK FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wyj\|5wyj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wyj\|5wyj]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/rRNA_small_subunit_pseudouridine_methyltransferase_Nep1 rRNA small subunit pseudouridine methyltransferase Nep1], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.260 2.1.1.260] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/rRNA_small_subunit_pseudouridine_methyltransferase_Nep1 rRNA small subunit pseudouridine methyltransferase Nep1], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.260 2.1.1.260] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5wyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wyk OCA], [http://pdbe.org/5wyk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wyk RCSB], [http://www.ebi.ac.uk/pdbsum/5wyk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wyk ProSAT]</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=5wyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wyk OCA], [http://pdbe.org/5wyk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wyk RCSB], [http://www.ebi.ac.uk/pdbsum/5wyk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wyk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RRP7_YEAST RRP7_YEAST]] Plays an important role in the synthesis of 18S rRNA but is not required for the 5.8S and 25S pathway. Is necessary for the cleavage at site A2. Is required for efficient association of RPS27 with the pre-ribosomal particle. [[http://www.uniprot.org/uniprot/IMP3_YEAST IMP3_YEAST]] Required for the early cleavages at sites A0, A1 and A2 during 18S ribosomal pre-RNA processing.<ref>PMID:10409734</ref> <ref>PMID:15489263~~</ref> [[http://www.uniprot.org/uniprot/UTP12_YEAST UTP12_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309~~</ref> [[http://www.uniprot.org/uniprot/FBRL_YEAST FBRL_YEAST]] S-adenosyl-L-methionine-dependent methyltransferase that has the ability to methylate both RNAs and proteins. Involved in pre-rRNA processing by catalyzing the site-specific 2'-hydroxyl methylation of ribose moieties in pre-ribosomal RNA (PubMed:1825809). Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA. Involved in the biogenesis of the 18S rRNA. Also acts as a protein methyltransferase by mediating methylation of 'Gln-105' of histone H2A (H2AQ105me), a modification that impairs binding of the FACT complex and is specifically present at 35S ribosomal DNA locus (PubMed:24352239).<ref>PMID:1825809</ref> <ref>PMID:24352239</ref> <ref>PMID:2686980</ref> [[http://www.uniprot.org/uniprot/UTP13_YEAST UTP13_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309</ref> [[http://www.uniprot.org/uniprot/RCL1_YEAST RCL1_YEAST]] Does not have cyclase activity. Plays a role in 40S-ribosomal-subunit biogenesis in the early pre-rRNA processing steps at sites A0, A1 and A2 that are required for proper maturation of the 18S RNA. Essential for viability. [[http://www.uniprot.org/uniprot/PWP2_YEAST PWP2_YEAST]] Required for bud-site selection and cell separation. Also involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309</ref> <ref>PMID:8804409</ref> [[http://www.uniprot.org/uniprot/IMP4_YEAST IMP4_YEAST]] Required for the early cleavages at sites A0, A1 and A2 during 18S ribosomal pre-RNA processing.<ref>PMID:10409734</ref> <ref>PMID:15489263</ref> [[http://www.uniprot.org/uniprot/KRR1_YEAST KRR1_YEAST]] Required for 40S ribosome biogenesis. Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. Essential for vegetative growth.<ref>PMID:11996121</ref> <ref>PMID:11027267</ref> <ref>PMID:15094838</ref> <ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/UTP21_YEAST UTP21_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/UTP22_YEAST UTP22_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/NEP1_YEAST NEP1_YEAST]] S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates pseudouridine at position 1189 (Psi1189) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S rRNA. N1-methylation is independent on acp-modification at the N3-position of U1191. Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 (RPS19A/RPS19B) during the formation of pre-ribosomes.<ref>PMID:11694595</ref> <ref>PMID:11935223</ref> <ref>PMID:15590835</ref> <ref>PMID:20972225</ref> <ref>PMID:21087996</ref> [[http://www.uniprot.org/uniprot/PNO1_YEAST PNO1_YEAST]] Required for small ribosomal subunit (SSU) synthesis. Has a role in the processing of early nucleolar and late cytoplasmic pre-RNA species. Recruits DIM1 to nucleolar pre-RNAs. Indirectly required for cleavage at the A2 site of the 20S pre-rRNA, forming 18S rRNA, and at A1 and A2 sites of other pre-rRNAs.<ref>PMID:12502737</ref> <ref>PMID:12736301</ref> <ref>PMID:15037774</ref> [[http://www.uniprot.org/uniprot/SNU13_YEAST SNU13_YEAST]] Common component of the spliceosome and rRNA processing machinery. In association with the spliceosomal U4/U6.U5 tri-snRNP particle, required for splicing of pre-mRNA. In association with box C/D snoRNPs, required for processing of pre-ribosomal RNA (rRNA) and site-specific 2'-O-methylation of substrate RNAs. Essential for the accumulation and stability of U4 snRNA, U6 snRNA, and box C/D snoRNAs.<ref>PMID:11081632</ref> <ref>PMID:12215523</ref> <ref>PMID:14730029</ref> [[http://www.uniprot.org/uniprot/~~RS7A_YEAST RS7A_YEAST~~]] ~~Involved in nucleolar processing of pre-18S~~ ribosomal ~~RNA and ribosome assembly~~.<ref>PMID:~~15590835~~</ref> [[http://www.uniprot.org/uniprot/~~NOP56_YEAST NOP56_YEAST~~]] ~~Required for 60S~~ ribosomal ~~subunit synthesis~~.<ref>PMID:~~9372940~~</ref> [[http://www.uniprot.org/uniprot/FCF1_YEAST FCF1_YEAST]] Essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly. Required for the early cleavage steps of 35S rRNA at the A(0), A(1), and A(2) sites.<ref>PMID:16762320</ref> [[http://www.uniprot.org/uniprot/RS14A_YEAST RS14A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/UTP10_YEAST UTP10_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for optimal pre-ribosomal RNA transcription by RNA polymerase I together with a subset of U3 proteins required for transcription (t-UTPs). Involved in ribosome biosynthesis.<ref>PMID:12068309</ref> <ref>PMID:15489292</ref> <ref>PMID:16544271</ref> <ref>PMID:17652137</ref> [[http://www.uniprot.org/uniprot/BMS1_YEAST BMS1_YEAST]] May act as a molecular switch during maturation of the 40S ribosomal subunit in the nucleolus. The depletion of BMS1 interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits.<ref>PMID:11565748</ref> <ref>PMID:11565749</ref> [[http://www.uniprot.org/uniprot/RL1D1_YEAST RL1D1_YEAST]] Involved in rRNA-processing and ribosome biosynthesis.<ref>PMID:16544271</ref> [[http://www.uniprot.org/uniprot/RS9A_YEAST RS9A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/NOP58_YEAST NOP58_YEAST]] Required for pre-18S rRNA processing. May bind microtubules.<ref>PMID:9372940</ref> <ref>PMID:9632712</ref> [[http://www.uniprot.org/uniprot/UTP18_YEAST UTP18_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/RRP9_YEAST RRP9_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for efficient pre-rRNA cleavage at sites A0, A1 and A2, and biosynthesis of 18S rRNA.<ref>PMID:11105764</ref>	+	[[http://www.uniprot.org/uniprot/RRP7_YEAST RRP7_YEAST]] Plays an important role in the synthesis of 18S rRNA but is not required for the 5.8S and 25S pathway. Is necessary for the cleavage at site A2. Is required for efficient association of RPS27 with the pre-ribosomal particle. [[http://www.uniprot.org/uniprot/IMP3_YEAST IMP3_YEAST]] Required for the early cleavages at sites A0, A1 and A2 during 18S ribosomal pre-RNA processing.<ref>PMID:10409734</ref> <ref>PMID:15489263</ref> [[http://www.uniprot.org/uniprot/FBRL_YEAST FBRL_YEAST]] S-adenosyl-L-methionine-dependent methyltransferase that has the ability to methylate both RNAs and proteins. Involved in pre-rRNA processing by catalyzing the site-specific 2'-hydroxyl methylation of ribose moieties in pre-ribosomal RNA (PubMed:1825809). Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA. Involved in the biogenesis of the 18S rRNA. Also acts as a protein methyltransferase by mediating methylation of 'Gln-105' of histone H2A (H2AQ105me), a modification that impairs binding of the FACT complex and is specifically present at 35S ribosomal DNA locus (PubMed:24352239).<ref>PMID:1825809</ref> <ref>PMID:24352239</ref> <ref>PMID:2686980</ref> [[http://www.uniprot.org/uniprot/UTP12_YEAST UTP12_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309</ref> [[http://www.uniprot.org/uniprot/UTP13_YEAST UTP13_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309</ref> [[http://www.uniprot.org/uniprot/RCL1_YEAST RCL1_YEAST]] Does not have cyclase activity. Plays a role in 40S-ribosomal-subunit biogenesis in the early pre-rRNA processing steps at sites A0, A1 and A2 that are required for proper maturation of the 18S RNA. Essential for viability. [[http://www.uniprot.org/uniprot/PWP2_YEAST PWP2_YEAST]] Required for bud-site selection and cell separation. Also involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309</ref> <ref>PMID:8804409</ref> [[http://www.uniprot.org/uniprot/IMP4_YEAST IMP4_YEAST]] Required for the early cleavages at sites A0, A1 and A2 during 18S ribosomal pre-RNA processing.<ref>PMID:10409734</ref> <ref>PMID:15489263</ref> [[http://www.uniprot.org/uniprot/KRR1_YEAST KRR1_YEAST]] Required for 40S ribosome biogenesis. Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. Essential for vegetative growth.<ref>PMID:11996121</ref> <ref>PMID:11027267</ref> <ref>PMID:15094838</ref> <ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/UTP21_YEAST UTP21_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/UTP22_YEAST UTP22_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/NEP1_YEAST NEP1_YEAST]] S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates pseudouridine at position 1189 (Psi1189) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S rRNA. N1-methylation is independent on acp-modification at the N3-position of U1191. Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 (RPS19A/RPS19B) during the formation of pre-ribosomes.<ref>PMID:11694595</ref> <ref>PMID:11935223</ref> <ref>PMID:15590835</ref> <ref>PMID:20972225</ref> <ref>PMID:21087996</ref> [[http://www.uniprot.org/uniprot/PNO1_YEAST PNO1_YEAST]] Required for small ribosomal subunit (SSU) synthesis. Has a role in the processing of early nucleolar and late cytoplasmic pre-RNA species. Recruits DIM1 to nucleolar pre-RNAs. Indirectly required for cleavage at the A2 site of the 20S pre-rRNA, forming 18S rRNA, and at A1 and A2 sites of other pre-rRNAs.<ref>PMID:12502737</ref> <ref>PMID:12736301</ref> <ref>PMID:15037774</ref> [[http://www.uniprot.org/uniprot/SNU13_YEAST SNU13_YEAST]] Common component of the spliceosome and rRNA processing machinery. In association with the spliceosomal U4/U6.U5 tri-snRNP particle, required for splicing of pre-mRNA. In association with box C/D snoRNPs, required for processing of pre-ribosomal RNA (rRNA) and site-specific 2'-O-methylation of substrate RNAs. Essential for the accumulation and stability of U4 snRNA, U6 snRNA, and box C/D snoRNAs.<ref>PMID:11081632</ref> <ref>PMID:12215523</ref> <ref>PMID:14730029</ref> [[http://www.uniprot.org/uniprot/NOP56_YEAST NOP56_YEAST]] Required for 60S ribosomal subunit synthesis.<ref>PMID:9372940</ref> [[http://www.uniprot.org/uniprot/RS7A_YEAST RS7A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/FCF1_YEAST FCF1_YEAST]] Essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly. Required for the early cleavage steps of 35S rRNA at the A(0), A(1), and A(2) sites.<ref>PMID:16762320</ref> [[http://www.uniprot.org/uniprot/RS14A_YEAST RS14A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/UTP10_YEAST UTP10_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for optimal pre-ribosomal RNA transcription by RNA polymerase I together with a subset of U3 proteins required for transcription (t-UTPs). Involved in ribosome biosynthesis.<ref>PMID:12068309</ref> <ref>PMID:15489292</ref> <ref>PMID:16544271</ref> <ref>PMID:17652137</ref> [[http://www.uniprot.org/uniprot/BMS1_YEAST BMS1_YEAST]] May act as a molecular switch during maturation of the 40S ribosomal subunit in the nucleolus. The depletion of BMS1 interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits.<ref>PMID:11565748</ref> <ref>PMID:11565749</ref> [[http://www.uniprot.org/uniprot/RL1D1_YEAST RL1D1_YEAST]] Involved in rRNA-processing and ribosome biosynthesis.<ref>PMID:16544271</ref> [[http://www.uniprot.org/uniprot/RS9A_YEAST RS9A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/NOP58_YEAST NOP58_YEAST]] Required for pre-18S rRNA processing. May bind microtubules.<ref>PMID:9372940</ref> <ref>PMID:9632712</ref> [[http://www.uniprot.org/uniprot/UTP18_YEAST UTP18_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/RRP9_YEAST RRP9_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for efficient pre-rRNA cleavage at sites A0, A1 and A2, and biosynthesis of 18S rRNA.<ref>PMID:11105764</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 20:08, 6 March 2020

OCA — Fri, 06 Mar 2020 20:08:08 GMT

←Older revision		Revision as of 20:08, 6 March 2020
Line 1:		Line 1:
-	~~{{Large structure}}~~	+
	==Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)==		==Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)==
-	<~~StructureSection~~ load='5wyk' size='340' side='right' caption='[[5wyk]], [[Resolution\|resolution]] 4.50Å' scene=''>	+	<SX load='5wyk' size='340' side='right' viewer='molstar' caption='[[5wyk]], [[Resolution\|resolution]] 4.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wyk]] is a 58 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=5WYK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WYK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wyk]] is a 58 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] and [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=5WYK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WYK FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wyj\|5wyj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wyj\|5wyj]]</td></tr>
Line 9:		Line 9:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5wyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wyk OCA], [http://pdbe.org/5wyk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wyk RCSB], [http://www.ebi.ac.uk/pdbsum/5wyk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wyk ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5wyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wyk OCA], [http://pdbe.org/5wyk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wyk RCSB], [http://www.ebi.ac.uk/pdbsum/5wyk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wyk ProSAT]</span></td></tr>
	</table>		</table>
-	{{Large structure}}
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RRP7_YEAST RRP7_YEAST]] Plays an important role in the synthesis of 18S rRNA but is not required for the 5.8S and 25S pathway. Is necessary for the cleavage at site A2. Is required for efficient association of RPS27 with the pre-ribosomal particle. [[http://www.uniprot.org/uniprot/IMP3_YEAST IMP3_YEAST]] Required for the early cleavages at sites A0, A1 and A2 during 18S ribosomal pre-RNA processing.<ref>PMID:10409734</ref> <ref>PMID:15489263</ref> [[http://www.uniprot.org/uniprot/FBRL_YEAST FBRL_YEAST]] S-adenosyl-L-methionine-dependent methyltransferase that has the ability to methylate both RNAs and proteins. Involved in pre-rRNA processing by catalyzing the site-specific 2'-hydroxyl methylation of ribose moieties in pre-ribosomal RNA (PubMed:1825809). Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA. Involved in the biogenesis of the 18S rRNA. Also acts as a protein methyltransferase by mediating methylation of 'Gln-105' of histone H2A (H2AQ105me), a modification that impairs binding of the FACT complex and is specifically present at 35S ribosomal DNA locus (PubMed:24352239).<ref>PMID:1825809</ref> <ref>PMID:24352239</ref> <ref>PMID:2686980~~</ref> [[http://www.uniprot.org/uniprot/UTP12_YEAST UTP12_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309~~</ref> [[http://www.uniprot.org/uniprot/UTP13_YEAST UTP13_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309</ref> [[http://www.uniprot.org/uniprot/RCL1_YEAST RCL1_YEAST]] Does not have cyclase activity. Plays a role in 40S-ribosomal-subunit biogenesis in the early pre-rRNA processing steps at sites A0, A1 and A2 that are required for proper maturation of the 18S RNA. Essential for viability. [[http://www.uniprot.org/uniprot/PWP2_YEAST PWP2_YEAST]] Required for bud-site selection and cell separation. Also involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309</ref> <ref>PMID:8804409</ref> [[http://www.uniprot.org/uniprot/IMP4_YEAST IMP4_YEAST]] Required for the early cleavages at sites A0, A1 and A2 during 18S ribosomal pre-RNA processing.<ref>PMID:10409734</ref> <ref>PMID:15489263</ref> [[http://www.uniprot.org/uniprot/KRR1_YEAST KRR1_YEAST]] Required for 40S ribosome biogenesis. Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. Essential for vegetative growth.<ref>PMID:11996121</ref> <ref>PMID:11027267</ref> <ref>PMID:15094838</ref> <ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/UTP21_YEAST UTP21_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/UTP22_YEAST UTP22_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/NEP1_YEAST NEP1_YEAST]] S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates pseudouridine at position 1189 (Psi1189) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S rRNA. N1-methylation is independent on acp-modification at the N3-position of U1191. Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 (RPS19A/RPS19B) during the formation of pre-ribosomes.<ref>PMID:11694595</ref> <ref>PMID:11935223</ref> <ref>PMID:15590835</ref> <ref>PMID:20972225</ref> <ref>PMID:21087996</ref> [[http://www.uniprot.org/uniprot/PNO1_YEAST PNO1_YEAST]] Required for small ribosomal subunit (SSU) synthesis. Has a role in the processing of early nucleolar and late cytoplasmic pre-RNA species. Recruits DIM1 to nucleolar pre-RNAs. Indirectly required for cleavage at the A2 site of the 20S pre-rRNA, forming 18S rRNA, and at A1 and A2 sites of other pre-rRNAs.<ref>PMID:12502737</ref> <ref>PMID:12736301</ref> <ref>PMID:15037774</ref> [[http://www.uniprot.org/uniprot/SNU13_YEAST SNU13_YEAST]] Common component of the spliceosome and rRNA processing machinery. In association with the spliceosomal U4/U6.U5 tri-snRNP particle, required for splicing of pre-mRNA. In association with box C/D snoRNPs, required for processing of pre-ribosomal RNA (rRNA) and site-specific 2'-O-methylation of substrate RNAs. Essential for the accumulation and stability of U4 snRNA, U6 snRNA, and box C/D snoRNAs.<ref>PMID:11081632</ref> <ref>PMID:12215523</ref> <ref>PMID:14730029</ref> [[http://www.uniprot.org/uniprot/~~NOP56_YEAST NOP56_YEAST~~]] ~~Required for 60S~~ ribosomal ~~subunit synthesis~~.<ref>PMID:~~9372940~~</ref> [[http://www.uniprot.org/uniprot/~~RS7A_YEAST RS7A_YEAST~~]] ~~Involved in nucleolar processing of pre-18S~~ ribosomal ~~RNA and ribosome assembly~~.<ref>PMID:~~15590835~~</ref> [[http://www.uniprot.org/uniprot/FCF1_YEAST FCF1_YEAST]] Essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly. Required for the early cleavage steps of 35S rRNA at the A(0), A(1), and A(2) sites.<ref>PMID:16762320</ref> [[http://www.uniprot.org/uniprot/RS14A_YEAST RS14A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/UTP10_YEAST UTP10_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for optimal pre-ribosomal RNA transcription by RNA polymerase I together with a subset of U3 proteins required for transcription (t-UTPs). Involved in ribosome biosynthesis.<ref>PMID:12068309</ref> <ref>PMID:15489292</ref> <ref>PMID:16544271</ref> <ref>PMID:17652137</ref> [[http://www.uniprot.org/uniprot/BMS1_YEAST BMS1_YEAST]] May act as a molecular switch during maturation of the 40S ribosomal subunit in the nucleolus. The depletion of BMS1 interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits.<ref>PMID:11565748</ref> <ref>PMID:11565749</ref> [[http://www.uniprot.org/uniprot/RL1D1_YEAST RL1D1_YEAST]] Involved in rRNA-processing and ribosome biosynthesis.<ref>PMID:16544271</ref> [[http://www.uniprot.org/uniprot/RS9A_YEAST RS9A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/NOP58_YEAST NOP58_YEAST]] Required for pre-18S rRNA processing. May bind microtubules.<ref>PMID:9372940</ref> <ref>PMID:9632712</ref> [[http://www.uniprot.org/uniprot/UTP18_YEAST UTP18_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/RRP9_YEAST RRP9_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for efficient pre-rRNA cleavage at sites A0, A1 and A2, and biosynthesis of 18S rRNA.<ref>PMID:11105764</ref>	+	[[http://www.uniprot.org/uniprot/RRP7_YEAST RRP7_YEAST]] Plays an important role in the synthesis of 18S rRNA but is not required for the 5.8S and 25S pathway. Is necessary for the cleavage at site A2. Is required for efficient association of RPS27 with the pre-ribosomal particle. [[http://www.uniprot.org/uniprot/IMP3_YEAST IMP3_YEAST]] Required for the early cleavages at sites A0, A1 and A2 during 18S ribosomal pre-RNA processing.<ref>PMID:10409734</ref> <ref>PMID:15489263</ref> [[http://www.uniprot.org/uniprot/UTP12_YEAST UTP12_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309</ref> [[http://www.uniprot.org/uniprot/FBRL_YEAST FBRL_YEAST]] S-adenosyl-L-methionine-dependent methyltransferase that has the ability to methylate both RNAs and proteins. Involved in pre-rRNA processing by catalyzing the site-specific 2'-hydroxyl methylation of ribose moieties in pre-ribosomal RNA (PubMed:1825809). Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA. Involved in the biogenesis of the 18S rRNA. Also acts as a protein methyltransferase by mediating methylation of 'Gln-105' of histone H2A (H2AQ105me), a modification that impairs binding of the FACT complex and is specifically present at 35S ribosomal DNA locus (PubMed:24352239).<ref>PMID:1825809</ref> <ref>PMID:24352239</ref> <ref>PMID:2686980</ref> [[http://www.uniprot.org/uniprot/UTP13_YEAST UTP13_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309</ref> [[http://www.uniprot.org/uniprot/RCL1_YEAST RCL1_YEAST]] Does not have cyclase activity. Plays a role in 40S-ribosomal-subunit biogenesis in the early pre-rRNA processing steps at sites A0, A1 and A2 that are required for proper maturation of the 18S RNA. Essential for viability. [[http://www.uniprot.org/uniprot/PWP2_YEAST PWP2_YEAST]] Required for bud-site selection and cell separation. Also involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309</ref> <ref>PMID:8804409</ref> [[http://www.uniprot.org/uniprot/IMP4_YEAST IMP4_YEAST]] Required for the early cleavages at sites A0, A1 and A2 during 18S ribosomal pre-RNA processing.<ref>PMID:10409734</ref> <ref>PMID:15489263</ref> [[http://www.uniprot.org/uniprot/KRR1_YEAST KRR1_YEAST]] Required for 40S ribosome biogenesis. Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. Essential for vegetative growth.<ref>PMID:11996121</ref> <ref>PMID:11027267</ref> <ref>PMID:15094838</ref> <ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/UTP21_YEAST UTP21_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/UTP22_YEAST UTP22_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/NEP1_YEAST NEP1_YEAST]] S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates pseudouridine at position 1189 (Psi1189) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S rRNA. N1-methylation is independent on acp-modification at the N3-position of U1191. Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 (RPS19A/RPS19B) during the formation of pre-ribosomes.<ref>PMID:11694595</ref> <ref>PMID:11935223</ref> <ref>PMID:15590835</ref> <ref>PMID:20972225</ref> <ref>PMID:21087996</ref> [[http://www.uniprot.org/uniprot/PNO1_YEAST PNO1_YEAST]] Required for small ribosomal subunit (SSU) synthesis. Has a role in the processing of early nucleolar and late cytoplasmic pre-RNA species. Recruits DIM1 to nucleolar pre-RNAs. Indirectly required for cleavage at the A2 site of the 20S pre-rRNA, forming 18S rRNA, and at A1 and A2 sites of other pre-rRNAs.<ref>PMID:12502737</ref> <ref>PMID:12736301</ref> <ref>PMID:15037774</ref> [[http://www.uniprot.org/uniprot/SNU13_YEAST SNU13_YEAST]] Common component of the spliceosome and rRNA processing machinery. In association with the spliceosomal U4/U6.U5 tri-snRNP particle, required for splicing of pre-mRNA. In association with box C/D snoRNPs, required for processing of pre-ribosomal RNA (rRNA) and site-specific 2'-O-methylation of substrate RNAs. Essential for the accumulation and stability of U4 snRNA, U6 snRNA, and box C/D snoRNAs.<ref>PMID:11081632</ref> <ref>PMID:12215523</ref> <ref>PMID:14730029</ref> [[http://www.uniprot.org/uniprot/RS7A_YEAST RS7A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/NOP56_YEAST NOP56_YEAST]] Required for 60S ribosomal subunit synthesis.<ref>PMID:9372940</ref> [[http://www.uniprot.org/uniprot/FCF1_YEAST FCF1_YEAST]] Essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly. Required for the early cleavage steps of 35S rRNA at the A(0), A(1), and A(2) sites.<ref>PMID:16762320</ref> [[http://www.uniprot.org/uniprot/RS14A_YEAST RS14A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/UTP10_YEAST UTP10_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for optimal pre-ribosomal RNA transcription by RNA polymerase I together with a subset of U3 proteins required for transcription (t-UTPs). Involved in ribosome biosynthesis.<ref>PMID:12068309</ref> <ref>PMID:15489292</ref> <ref>PMID:16544271</ref> <ref>PMID:17652137</ref> [[http://www.uniprot.org/uniprot/BMS1_YEAST BMS1_YEAST]] May act as a molecular switch during maturation of the 40S ribosomal subunit in the nucleolus. The depletion of BMS1 interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits.<ref>PMID:11565748</ref> <ref>PMID:11565749</ref> [[http://www.uniprot.org/uniprot/RL1D1_YEAST RL1D1_YEAST]] Involved in rRNA-processing and ribosome biosynthesis.<ref>PMID:16544271</ref> [[http://www.uniprot.org/uniprot/RS9A_YEAST RS9A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/NOP58_YEAST NOP58_YEAST]] Required for pre-18S rRNA processing. May bind microtubules.<ref>PMID:9372940</ref> <ref>PMID:9632712</ref> [[http://www.uniprot.org/uniprot/UTP18_YEAST UTP18_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/RRP9_YEAST RRP9_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for efficient pre-rRNA cleavage at sites A0, A1 and A2, and biosynthesis of 18S rRNA.<ref>PMID:11105764</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5wyk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5wyk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribosome 3D structures\|Ribosome 3D structures]]
		+	*[[Ribosome biogenesis protein\|Ribosome biogenesis protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
		+	[[Category: Baker's yeast]]
		+	[[Category: Large Structures]]
	[[Category: RRNA small subunit pseudouridine methyltransferase Nep1]]		[[Category: RRNA small subunit pseudouridine methyltransferase Nep1]]
	[[Category: Sun, Q]]		[[Category: Sun, Q]]

OCA at 09:02, 17 May 2017

OCA — Wed, 17 May 2017 09:02:09 GMT

←Older revision		Revision as of 09:02, 17 May 2017
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	{{Large structure}}
		+	==Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)==
		+	<StructureSection load='5wyk' size='340' side='right' caption='[[5wyk]], [[Resolution\|resolution]] 4.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5wyk]] is a 58 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=5WYK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WYK FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wyj\|5wyj]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/rRNA_small_subunit_pseudouridine_methyltransferase_Nep1 rRNA small subunit pseudouridine methyltransferase Nep1], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.260 2.1.1.260] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5wyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wyk OCA], [http://pdbe.org/5wyk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wyk RCSB], [http://www.ebi.ac.uk/pdbsum/5wyk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wyk ProSAT]</span></td></tr>
		+	</table>
		+	{{Large structure}}
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RRP7_YEAST RRP7_YEAST]] Plays an important role in the synthesis of 18S rRNA but is not required for the 5.8S and 25S pathway. Is necessary for the cleavage at site A2. Is required for efficient association of RPS27 with the pre-ribosomal particle. [[http://www.uniprot.org/uniprot/IMP3_YEAST IMP3_YEAST]] Required for the early cleavages at sites A0, A1 and A2 during 18S ribosomal pre-RNA processing.<ref>PMID:10409734</ref> <ref>PMID:15489263</ref> [[http://www.uniprot.org/uniprot/FBRL_YEAST FBRL_YEAST]] S-adenosyl-L-methionine-dependent methyltransferase that has the ability to methylate both RNAs and proteins. Involved in pre-rRNA processing by catalyzing the site-specific 2'-hydroxyl methylation of ribose moieties in pre-ribosomal RNA (PubMed:1825809). Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA. Involved in the biogenesis of the 18S rRNA. Also acts as a protein methyltransferase by mediating methylation of 'Gln-105' of histone H2A (H2AQ105me), a modification that impairs binding of the FACT complex and is specifically present at 35S ribosomal DNA locus (PubMed:24352239).<ref>PMID:1825809</ref> <ref>PMID:24352239</ref> <ref>PMID:2686980</ref> [[http://www.uniprot.org/uniprot/UTP12_YEAST UTP12_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309</ref> [[http://www.uniprot.org/uniprot/UTP13_YEAST UTP13_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309</ref> [[http://www.uniprot.org/uniprot/RCL1_YEAST RCL1_YEAST]] Does not have cyclase activity. Plays a role in 40S-ribosomal-subunit biogenesis in the early pre-rRNA processing steps at sites A0, A1 and A2 that are required for proper maturation of the 18S RNA. Essential for viability. [[http://www.uniprot.org/uniprot/PWP2_YEAST PWP2_YEAST]] Required for bud-site selection and cell separation. Also involved in nucleolar processing of pre-18S ribosomal RNA.<ref>PMID:12068309</ref> <ref>PMID:8804409</ref> [[http://www.uniprot.org/uniprot/IMP4_YEAST IMP4_YEAST]] Required for the early cleavages at sites A0, A1 and A2 during 18S ribosomal pre-RNA processing.<ref>PMID:10409734</ref> <ref>PMID:15489263</ref> [[http://www.uniprot.org/uniprot/KRR1_YEAST KRR1_YEAST]] Required for 40S ribosome biogenesis. Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. Essential for vegetative growth.<ref>PMID:11996121</ref> <ref>PMID:11027267</ref> <ref>PMID:15094838</ref> <ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/UTP21_YEAST UTP21_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/UTP22_YEAST UTP22_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/NEP1_YEAST NEP1_YEAST]] S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates pseudouridine at position 1189 (Psi1189) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S rRNA. N1-methylation is independent on acp-modification at the N3-position of U1191. Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 (RPS19A/RPS19B) during the formation of pre-ribosomes.<ref>PMID:11694595</ref> <ref>PMID:11935223</ref> <ref>PMID:15590835</ref> <ref>PMID:20972225</ref> <ref>PMID:21087996</ref> [[http://www.uniprot.org/uniprot/PNO1_YEAST PNO1_YEAST]] Required for small ribosomal subunit (SSU) synthesis. Has a role in the processing of early nucleolar and late cytoplasmic pre-RNA species. Recruits DIM1 to nucleolar pre-RNAs. Indirectly required for cleavage at the A2 site of the 20S pre-rRNA, forming 18S rRNA, and at A1 and A2 sites of other pre-rRNAs.<ref>PMID:12502737</ref> <ref>PMID:12736301</ref> <ref>PMID:15037774</ref> [[http://www.uniprot.org/uniprot/SNU13_YEAST SNU13_YEAST]] Common component of the spliceosome and rRNA processing machinery. In association with the spliceosomal U4/U6.U5 tri-snRNP particle, required for splicing of pre-mRNA. In association with box C/D snoRNPs, required for processing of pre-ribosomal RNA (rRNA) and site-specific 2'-O-methylation of substrate RNAs. Essential for the accumulation and stability of U4 snRNA, U6 snRNA, and box C/D snoRNAs.<ref>PMID:11081632</ref> <ref>PMID:12215523</ref> <ref>PMID:14730029</ref> [[http://www.uniprot.org/uniprot/NOP56_YEAST NOP56_YEAST]] Required for 60S ribosomal subunit synthesis.<ref>PMID:9372940</ref> [[http://www.uniprot.org/uniprot/RS7A_YEAST RS7A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/FCF1_YEAST FCF1_YEAST]] Essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly. Required for the early cleavage steps of 35S rRNA at the A(0), A(1), and A(2) sites.<ref>PMID:16762320</ref> [[http://www.uniprot.org/uniprot/RS14A_YEAST RS14A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/UTP10_YEAST UTP10_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for optimal pre-ribosomal RNA transcription by RNA polymerase I together with a subset of U3 proteins required for transcription (t-UTPs). Involved in ribosome biosynthesis.<ref>PMID:12068309</ref> <ref>PMID:15489292</ref> <ref>PMID:16544271</ref> <ref>PMID:17652137</ref> [[http://www.uniprot.org/uniprot/BMS1_YEAST BMS1_YEAST]] May act as a molecular switch during maturation of the 40S ribosomal subunit in the nucleolus. The depletion of BMS1 interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits.<ref>PMID:11565748</ref> <ref>PMID:11565749</ref> [[http://www.uniprot.org/uniprot/RL1D1_YEAST RL1D1_YEAST]] Involved in rRNA-processing and ribosome biosynthesis.<ref>PMID:16544271</ref> [[http://www.uniprot.org/uniprot/RS9A_YEAST RS9A_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/NOP58_YEAST NOP58_YEAST]] Required for pre-18S rRNA processing. May bind microtubules.<ref>PMID:9372940</ref> <ref>PMID:9632712</ref> [[http://www.uniprot.org/uniprot/UTP18_YEAST UTP18_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.<ref>PMID:15590835</ref> [[http://www.uniprot.org/uniprot/RRP9_YEAST RRP9_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for efficient pre-rRNA cleavage at sites A0, A1 and A2, and biosynthesis of 18S rRNA.<ref>PMID:11105764</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of Saccharomyces cerevisiae 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors.

-	~~The entry 5wyk is ON HOLD~~	+	Molecular architecture of the 90S small subunit pre-ribosome.,Sun Q, Zhu X, Qi J, An W, Lan P, Tan D, Chen R, Wang B, Zheng S, Zhang C, Chen X, Zhang W, Chen J, Dong MQ, Ye K Elife. 2017 Feb 28;6. pii: e22086. doi: 10.7554/eLife.22086. PMID:28244370<ref>PMID:28244370</ref>

-	~~Authors: Ye~~, K.~~, Zhu, X~~.~~, Sun, Q~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Cryo~~-~~EM structure of the 90S~~ small subunit ~~pre-ribosome (Mtr4-depleted, Enp1-TAP)~~	+	<div class="pdbe-citations 5wyk" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: RRNA small subunit pseudouridine methyltransferase Nep1]]
		+	[[Category: Sun, Q]]
	[[Category: Ye, K]]		[[Category: Ye, K]]
	[[Category: Zhu, X]]		[[Category: Zhu, X]]
-	[[Category: ~~Sun, Q~~]]	+	[[Category: Pre-ribosome]]
		+	[[Category: Protein-rna complex]]
		+	[[Category: Ribosome]]

OCA at 19:59, 15 March 2017

OCA — Wed, 15 Mar 2017 19:59:31 GMT

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	Description: Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)		Description: Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Sun, Q]]
	[[Category: Ye, K]]		[[Category: Ye, K]]
	[[Category: Zhu, X]]		[[Category: Zhu, X]]
		+	[[Category: Sun, Q]]

OCA: Protected "5wyk" [edit=sysop:move=sysop]

OCA — Wed, 18 Jan 2017 15:21:49 GMT

Protected "5wyk" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:21, 18 January 2017

OCA: New page: '''Unreleased structure''' The entry 5wyk is ON HOLD Authors: Ye, K., Zhu, X., Sun, Q. Description: Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP) [[...

OCA — Wed, 18 Jan 2017 15:21:48 GMT

New page: '''Unreleased structure''' The entry 5wyk is ON HOLD Authors: Ye, K., Zhu, X., Sun, Q. Description: Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP) [[...

New page

'''Unreleased structure'''

The entry 5wyk is ON HOLD

Authors: Ye, K., Zhu, X., Sun, Q.

Description: Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)
[[Category: Unreleased Structures]]
[[Category: Sun, Q]]
[[Category: Ye, K]]
[[Category: Zhu, X]]