2v3m

From Proteopedia

(Difference between revisions)

Current revision

Structure of the Gar1 domain of NAf1

Structural highlights

2v3m is a 6 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.74Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NAF1_YEAST RNA-binding protein required for the maturation of box H/ACA snoRNPs complex and ribosome biogenesis. During assembly of the H/ACA snoRNPs complex, it associates with the complex and disappears during maturation of the complex and is replaced by GAR1 to yield mature H/ACA snoRNPs complex. Acts as a competitive binder for CBF5 probably required to prevent non-cognate RNAs from being loaded during transport of the particle by inducing a non-productive conformation of CBF5.^[1] ^[2] ^[3] ^[4] ^[5]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Naf1 is an essential protein involved in the maturation of box H/ACA ribonucleoproteins, a group of particles required for ribosome biogenesis, modification of spliceosomal small nuclear RNAs and telomere synthesis. Naf1 participates in the assembly of the RNP at transcription sites and in the nuclear trafficking of the complex. The crystal structure of a domain of yeast Naf1p, Naf1Delta1p, reveals a striking structural homology with the core domain of archaeal Gar1, an essential protein component of the mature RNP; it suggests that Naf1p and Gar1p have a common binding site on the enzymatic protein component of the particle, Cbf5p. We propose that Naf1p is a competitive binder for Cbf5p, which is replaced by Gar1p during maturation of the H/ACA particle. The exchange of Naf1p by Gar1p might be prompted by external factors that alter the oligomerisation state of Naf1p and Gar1p. The structural homology with Gar1 suggests that the function of Naf1 involves preventing non-cognate RNAs from being loaded during transport of the particle by inducing a non-productive conformation of Cbf5.

The box H/ACA RNP assembly factor Naf1p contains a domain homologous to Gar1p mediating its interaction with Cbf5p.,Leulliot N, Godin KS, Hoareau-Aveilla C, Quevillon-Cheruel S, Varani G, Henry Y, Van Tilbeurgh H J Mol Biol. 2007 Aug 31;371(5):1338-53. Epub 2007 Jun 16. PMID:17612558^[6]

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

References

↑ Yang PK, Rotondo G, Porras T, Legrain P, Chanfreau G. The Shq1p.Naf1p complex is required for box H/ACA small nucleolar ribonucleoprotein particle biogenesis. J Biol Chem. 2002 Nov 22;277(47):45235-42. Epub 2002 Sep 11. PMID:12228251 doi:10.1074/jbc.M207669200
↑ Dez C, Noaillac-Depeyre J, Caizergues-Ferrer M, Henry Y. Naf1p, an essential nucleoplasmic factor specifically required for accumulation of box H/ACA small nucleolar RNPs. Mol Cell Biol. 2002 Oct;22(20):7053-65. PMID:12242285
↑ Fatica A, Dlakic M, Tollervey D. Naf1 p is a box H/ACA snoRNP assembly factor. RNA. 2002 Dec;8(12):1502-14. PMID:12515383
↑ Yang PK, Hoareau C, Froment C, Monsarrat B, Henry Y, Chanfreau G. Cotranscriptional recruitment of the pseudouridylsynthetase Cbf5p and of the RNA binding protein Naf1p during H/ACA snoRNP assembly. Mol Cell Biol. 2005 Apr;25(8):3295-304. PMID:15798213 doi:http://dx.doi.org/10.1128/MCB.25.8.3295-3304.2005
↑ Ballarino M, Morlando M, Pagano F, Fatica A, Bozzoni I. The cotranscriptional assembly of snoRNPs controls the biosynthesis of H/ACA snoRNAs in Saccharomyces cerevisiae. Mol Cell Biol. 2005 Jul;25(13):5396-403. PMID:15964797 doi:http://dx.doi.org/25/13/5396
↑ Leulliot N, Godin KS, Hoareau-Aveilla C, Quevillon-Cheruel S, Varani G, Henry Y, Van Tilbeurgh H. The box H/ACA RNP assembly factor Naf1p contains a domain homologous to Gar1p mediating its interaction with Cbf5p. J Mol Biol. 2007 Aug 31;371(5):1338-53. Epub 2007 Jun 16. PMID:17612558 doi:S0022-2836(07)00822-4

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2v3m"

@@ Line 1: / Line 1: @@
-==STRUCTURE OF THE GAR1 DOMAIN OF NAF1==
-<StructureSection load='2v3m' size='340' side='right' caption='[[2v3m]], [[Resolution|resolution]] 2.74&Aring;' scene=''>
+==Structure of the Gar1 domain of NAf1==
+<StructureSection load='2v3m' size='340' side='right'caption='[[2v3m]], [[Resolution|resolution]] 2.74&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2v3m]] is a 6 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=2V3M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V3M FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2v3m]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V3M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V3M FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.74&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=2v3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v3m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v3m RCSB], [http://www.ebi.ac.uk/pdbsum/2v3m PDBsum]</span></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=2v3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v3m OCA], [https://pdbe.org/2v3m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v3m RCSB], [https://www.ebi.ac.uk/pdbsum/2v3m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v3m ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/NAF1_YEAST NAF1_YEAST] RNA-binding protein required for the maturation of box H/ACA snoRNPs complex and ribosome biogenesis. During assembly of the H/ACA snoRNPs complex, it associates with the complex and disappears during maturation of the complex and is replaced by GAR1 to yield mature H/ACA snoRNPs complex. Acts as a competitive binder for CBF5 probably required to prevent non-cognate RNAs from being loaded during transport of the particle by inducing a non-productive conformation of CBF5.<ref>PMID:12228251</ref> <ref>PMID:12242285</ref> <ref>PMID:12515383</ref> <ref>PMID:15798213</ref> <ref>PMID:15964797</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v3/2v3m_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v3/2v3m_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2v3m ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2v3m" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Godin, K S.]]
+[[Category: Godin KS]]
-[[Category: Henry, Y.]]
+[[Category: Henry Y]]
-[[Category: Hoareau-Aveilla, C.]]
+[[Category: Hoareau-Aveilla C]]
-[[Category: Leulliot, N.]]
+[[Category: Leulliot N]]
-[[Category: Quevillon-Cheruel, S.]]
+[[Category: Quevillon-Cheruel S]]
-[[Category: Tilbeurgh, H Van.]]
+[[Category: Varani G]]
-[[Category: Varani, G.]]
+[[Category: Van Tilbeurgh H]]
-[[Category: Gar1]]
-[[Category: Hypothetical protein]]
-[[Category: Naf1]]
-[[Category: Phosphorylation]]
-[[Category: Ribosomal protein]]
-[[Category: Snornp]]

2v3m

From Proteopedia

Current revision

Structure of the Gar1 domain of NAf1

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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