3j16

From Proteopedia

(Difference between revisions)

Revision as of 17:40, 10 April 2020

Models of ribosome-bound Dom34p and Rli1p and their ribosomal binding partners

3j16, resolution 7.20Å

Structural highlights

3j16 is a 12 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	3j15
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RS6A_YEAST] Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.^[1] [RLI1_YEAST] Component of the multifactor complex (MFC) involved in translation initiation. Required for the binding of MFC to the 40S ribosome. Required for the processing and nuclear export of the 60S and 40S ribosomal subunits.^[2] ^[3] ^[4] [RLA0_YEAST] Ribosomal protein P0 is the functional equivalent of E.coli protein L10. [DOM34_YEAST] Involved in protein translation. Together with HBS1, may function in recognizing stalled ribosomes and triggering endonucleolytic cleavage of the mRNA, a mechanism to release non-functional ribosomes and degrade damaged mRNAs. The complex formed by DOM34 and HBS1 has ribonuclease activity towards double-stranded RNA substrates, but does not cleave single-stranded RNA. Acts as endonuclease; has no exonuclease activity. Increases the affinity of HBS1 for GTP, but nor for GDP. Promotes G1 progression and differentiation and is involved in mitotic and meiotic cell divisions.^[5] ^[6] ^[7] [RL12A_YEAST] This protein binds directly to 26S ribosomal RNA.[HAMAP-Rule:MF_00736]

Publication Abstract from PubMed

Ribosome-driven protein biosynthesis is comprised of four phases: initiation, elongation, termination and recycling. In bacteria, ribosome recycling requires ribosome recycling factor and elongation factor G, and several structures of bacterial recycling complexes have been determined. In the eukaryotic and archaeal kingdoms, however, recycling involves the ABC-type ATPase ABCE1 and little is known about its structural basis. Here we present cryo-electron microscopy reconstructions of eukaryotic and archaeal ribosome recycling complexes containing ABCE1 and the termination factor paralogue Pelota. These structures reveal the overall binding mode of ABCE1 to be similar to canonical translation factors. Moreover, the iron-sulphur cluster domain of ABCE1 interacts with and stabilizes Pelota in a conformation that reaches towards the peptidyl transferase centre, thus explaining how ABCE1 may stimulate peptide-release activity of canonical termination factors. Using the mechanochemical properties of ABCE1, a conserved mechanism in archaea and eukaryotes is suggested that couples translation termination to recycling, and eventually to re-initiation.

Structural basis of highly conserved ribosome recycling in eukaryotes and archaea.,Becker T, Franckenberg S, Wickles S, Shoemaker CJ, Anger AM, Armache JP, Sieber H, Ungewickell C, Berninghausen O, Daberkow I, Karcher A, Thomm M, Hopfner KP, Green R, Beckmann R Nature. 2012 Feb 22;482(7386):501-6. doi: 10.1038/nature10829. PMID:22358840^[8]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Bernstein KA, Gallagher JE, Mitchell BM, Granneman S, Baserga SJ. The small-subunit processome is a ribosome assembly intermediate. Eukaryot Cell. 2004 Dec;3(6):1619-26. PMID:15590835 doi:http://dx.doi.org/10.1128/EC.3.6.1619-1626.2004
↑ Dong J, Lai R, Nielsen K, Fekete CA, Qiu H, Hinnebusch AG. The essential ATP-binding cassette protein RLI1 functions in translation by promoting preinitiation complex assembly. J Biol Chem. 2004 Oct 1;279(40):42157-68. Epub 2004 Jul 23. PMID:15277527 doi:http://dx.doi.org/10.1074/jbc.M404502200
↑ Yarunin A, Panse VG, Petfalski E, Dez C, Tollervey D, Hurt EC. Functional link between ribosome formation and biogenesis of iron-sulfur proteins. EMBO J. 2005 Feb 9;24(3):580-8. Epub 2005 Jan 20. PMID:15660135 doi:http://dx.doi.org/10.1038/sj.emboj.7600540
↑ Kispal G, Sipos K, Lange H, Fekete Z, Bedekovics T, Janaky T, Bassler J, Aguilar Netz DJ, Balk J, Rotte C, Lill R. Biogenesis of cytosolic ribosomes requires the essential iron-sulphur protein Rli1p and mitochondria. EMBO J. 2005 Feb 9;24(3):589-98. Epub 2005 Jan 20. PMID:15660134 doi:http://dx.doi.org/10.1038/sj.emboj.7600541
↑ Doma MK, Parker R. Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature. 2006 Mar 23;440(7083):561-4. PMID:16554824 doi:nature04530
↑ Lee HH, Kim YS, Kim KH, Heo I, Kim SK, Kim O, Kim HK, Yoon JY, Kim HS, Kim do J, Lee SJ, Yoon HJ, Kim SJ, Lee BG, Song HK, Kim VN, Park CM, Suh SW. Structural and functional insights into Dom34, a key component of no-go mRNA decay. Mol Cell. 2007 Sep 21;27(6):938-50. PMID:17889667 doi:10.1016/j.molcel.2007.07.019
↑ Graille M, Chaillet M, van Tilbeurgh H. Structure of yeast Dom34: a protein related to translation termination factor Erf1 and involved in No-Go decay. J Biol Chem. 2008 Mar 14;283(11):7145-54. Epub 2008 Jan 7. PMID:18180287 doi:10.1074/jbc.M708224200
↑ Becker T, Franckenberg S, Wickles S, Shoemaker CJ, Anger AM, Armache JP, Sieber H, Ungewickell C, Berninghausen O, Daberkow I, Karcher A, Thomm M, Hopfner KP, Green R, Beckmann R. Structural basis of highly conserved ribosome recycling in eukaryotes and archaea. Nature. 2012 Feb 22;482(7386):501-6. doi: 10.1038/nature10829. PMID:22358840 doi:10.1038/nature10829

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3j16"

@@ Line 3: / Line 3: @@
 <SX load='3j16' size='340' side='right' viewer='molstar' caption='[[3j16]], [[Resolution|resolution]] 7.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3j16]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J16 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J16 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3j16]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J16 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3J16 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3j15|3j15]]</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=3j16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j16 OCA], [http://pdbe.org/3j16 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j16 RCSB], [http://www.ebi.ac.uk/pdbsum/3j16 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j16 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=3j16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j16 OCA], [http://pdbe.org/3j16 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j16 RCSB], [http://www.ebi.ac.uk/pdbsum/3j16 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j16 ProSAT]</span></td></tr>
 </table>
 == Function ==

3j16

From Proteopedia

Revision as of 17:40, 10 April 2020

Models of ribosome-bound Dom34p and Rli1p and their ribosomal binding partners

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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