5jcs: Difference between revisions

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<SX load='5jcs' size='340' side='right' viewer='molstar' caption='[[5jcs]], [[Resolution|resolution]] 9.50&Aring;' scene=''>
<SX load='5jcs' size='340' side='right' viewer='molstar' caption='[[5jcs]], [[Resolution|resolution]] 9.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5jcs]] is a 48 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JCS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JCS FirstGlance]. <br>
<table><tr><td colspan='2'>[[5jcs]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5fl8 5fl8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JCS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JCS FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RPL2A, RPL5B, YFR031C-A, YFR031BC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL34A, YER056C-A, YER056BC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL7A, RPL6A, RPL8A, YL8A, YGL076C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL35A, SOS1, YDL191W, D1249 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL8A, MAK7, RPL4A, YHL033C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL36A, RPL39A, YMR194W, YM9646.06 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL9A, RPL8A, RPL9, YGL147C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL37A, RPL35A, YLR185W, L9470.6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL1A, SSM1, SSM1A, YPL220W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL38, YLR325C, L8543.2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL11A, RP39A, RPL16A, YPR102C, P8283.14 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL30, RPL32, YGL030W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL39, RPL46, SPB2, YJL189W, J0360 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL12A, RPL15B, YEL054C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), TIF6, CDC95, YPR016C, LPZ15C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL13A, YDL082W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), MRT4, YKL009W, YKL160 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL14A, YKL006W, YKL153 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), NOG1, YPL093W, LPG15W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL15A, RPL10A, RPL13A, YL10A, YLR029C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL43A, YPR043W, YP9499.02 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL16A, RPL13, RPL21A, YIL133C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL3, MAK8, TCM1, YOR063W, YOR29-14 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RSA4, YCR072C, YCR72C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL17A, RPL17, RPL20A, YKL180W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), SDA1, YGR245C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL18A, RP28A, YOL120C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), MDN1, REA1, YLR106C, L2901, L8004.13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL19A, RPL23A, YL14A, YBR084C-A, YBR084BC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RLP24, YLR009W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL20A, RPL18A, RPL18A2, YMR242C, YM9408.04C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), ARX1, YDR101C, YD8557.10c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL21A, URP1, YBR191W, YBR1401 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL31A, RPL34, RPL34A, YDL075W, D2478 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL22A, YLR061W, L2168 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL23A, RPL17A, RPL17AA, YBL087C, YBL0713 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL25, YOL127W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL26A, RPL26, RPL33A, YLR344W, L8300.4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL27A, RPL27, YHR010W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL28, CYH2, YGL103W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL4A, RPL2, RPL2A, YBR031W, YBR0315 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL32, YBL092W, YBL0838 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL5, RPL1, RPL1A, YPL131W, LPI14W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL33A, RPL37A, YPL143W, LPI4W, P2625 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RPL6A, RPL17A, YL16A, YML073C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5jcs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jcs OCA], [https://pdbe.org/5jcs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jcs RCSB], [https://www.ebi.ac.uk/pdbsum/5jcs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jcs 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=5jcs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jcs OCA], [http://pdbe.org/5jcs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jcs RCSB], [http://www.ebi.ac.uk/pdbsum/5jcs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jcs ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/SDA1_YEAST SDA1_YEAST]] Required for 60S pre-ribosomal subunits export to the cytoplasm. May also be required for 60S ribosomal subunit maturation and accumulation. Involved in G1 events and passage through start, and possibly actin cytoskeleton organization.<ref>PMID:10704371</ref> <ref>PMID:11160833</ref> <ref>PMID:12374754</ref> <ref>PMID:15107621</ref> <ref>PMID:16541108</ref>  [[http://www.uniprot.org/uniprot/RL12A_YEAST RL12A_YEAST]] This protein binds directly to 26S ribosomal RNA.[HAMAP-Rule:MF_00736] [[http://www.uniprot.org/uniprot/RL5_YEAST RL5_YEAST]] Binds 5S RNA and is required for 60S subunit assembly. [[http://www.uniprot.org/uniprot/NOG1_YEAST NOG1_YEAST]] Involved in the biogenesis of the 60S ribosomal subunit.<ref>PMID:12808088</ref>  [[http://www.uniprot.org/uniprot/NLE1_YEAST NLE1_YEAST]] Involved in processing and efficient intra-nuclear transport or pre-60S ribosomal subunits. Forms a complex with REA1 which is essential for ATP-dependent dissociation of a group of nonribosomal factors from the pre-60S particle.<ref>PMID:16221974</ref> <ref>PMID:19737519</ref> <ref>PMID:20542003</ref>  [[http://www.uniprot.org/uniprot/RL37A_YEAST RL37A_YEAST]] Binds to the 23S rRNA (By similarity). [[http://www.uniprot.org/uniprot/MRT4_YEAST MRT4_YEAST]] Involved in mRNA turnover and ribosome assembly. [[http://www.uniprot.org/uniprot/IF6_YEAST IF6_YEAST]] Binds to the 60S ribosomal subunit and prevents its association with the 40S ribosomal subunit to form the 80S initiation complex in the cytoplasm. Is also involved in ribosome biogenesis. Associates with pre-60S subunits in the nucleus and is involved in its nuclear export. Cytoplasmic release of TIF6 from 60S subunits and nuclear relocalization is promoted by the GTPase RIA1/EFL1 and by SDO1. Also required for pre-rRNA processing.<ref>PMID:10085284</ref> <ref>PMID:11779510</ref> <ref>PMID:11238882</ref> <ref>PMID:17353896</ref> <ref>PMID:18256024</ref> <ref>PMID:11101899</ref>  [[http://www.uniprot.org/uniprot/RLP24_YEAST RLP24_YEAST]] Involved in the biogenesis of the 60S ribosomal subunit. Ensures the docking of NOG1 to pre-60S particles.<ref>PMID:12808088</ref>  [[http://www.uniprot.org/uniprot/ARX1_YEAST ARX1_YEAST]] Probable metalloprotease involved in proper assembly of pre-ribosomal particles during the biogenesis of the 60S ribosomal subunit. Accompanies the pre-60S particles to the cytoplasm.<ref>PMID:12374754</ref> <ref>PMID:16648468</ref>  [[http://www.uniprot.org/uniprot/MDN1_YEAST MDN1_YEAST]] Nuclear chaperone required for maturation and nuclear export of pre-60S ribosome subunits. Functions at successive maturation steps to remove ribosomal factors at critical transition points, first driving the exit of early pre-60S particles from the nucleolus and then driving late pre-60S particles from the nucleus. Mediates ATP-dependent remodeling of the pre-ribosome just prior to export to allow maturation of 60S subunits into export-competent particles. Removes the ribosome biogenesis factor RSA4 from pre-60S ribosomal subunits in the nucleoplasm to drive nuclear export of the subunit. Involved in 3' processing of the 5.8S rRNA.<ref>PMID:15260980</ref> <ref>PMID:15528184</ref> <ref>PMID:19737519</ref> <ref>PMID:20542003</ref>  [[http://www.uniprot.org/uniprot/RL25_YEAST RL25_YEAST]] This protein binds to a specific region on the 26S rRNA. [[http://www.uniprot.org/uniprot/RL11A_YEAST RL11A_YEAST]] Binds to 5S ribosomal RNA. [[http://www.uniprot.org/uniprot/RL4A_YEAST RL4A_YEAST]] Participates in the regulation of the accumulation of its own mRNA.<ref>PMID:2065661</ref> 
[https://www.uniprot.org/uniprot/RL16A_YEAST RL16A_YEAST]  
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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__TOC__
__TOC__
</SX>
</SX>
[[Category: Baker's yeast]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Barrio-Garcia, C]]
[[Category: Saccharomyces cerevisiae S288C]]
[[Category: Bassler, J]]
[[Category: Barrio-Garcia C]]
[[Category: Beckmann, R]]
[[Category: Bassler J]]
[[Category: Berninghausen, O]]
[[Category: Beckmann R]]
[[Category: Flemming, D]]
[[Category: Berninghausen O]]
[[Category: Hurt, E]]
[[Category: Flemming D]]
[[Category: Kater, L]]
[[Category: Hurt E]]
[[Category: Thoms, M]]
[[Category: Kater L]]
[[Category: Pre-60s ribosome rix1 rea1]]
[[Category: Thoms M]]
[[Category: Ribosome]]

Latest revision as of 13:16, 15 February 2023

CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLECRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE

5jcs, resolution 9.50Å

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