3lcn

From Proteopedia

(Difference between revisions)

Current revision

Nab2:Gfd1 complex

Structural highlights

3lcn is a 4 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 2Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NAB2_YEAST This essential protein binds to polyadenylated RNA and single-stranded DNA. It may be involved not only in RNA processing but also in transcription regulation. Believed to associate directly with nascent RNA polymerase II transcripts and remain associated during subsequent nuclear RNA processing reactions.

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

Following transcription, mRNA is processed, packaged into messenger ribonucleoprotein (mRNP) particles, and transported through nuclear pores (NPCs) to the cytoplasm. At the NPC cytoplasmic face, Dbp5 mediates mRNP remodeling and mRNA export factor dissociation, releasing transcripts for translation. In Saccharomyces cerevisiae, the conserved poly(A) RNA-binding protein, Nab2, facilitates NPC targeting of transcripts and also modulates poly(A) tail length. Dbp5 removes Nab2 from mRNPs at the cytoplasmic face of the pore and, importantly, a Nab2 RNA-binding mutant suppresses the thermosensitive rat8-2 (dbp5) mutant. GFD1 is a multicopy suppressor of rat8-2 (dbp5), and Gfd1 interacts physically with both Dbp5 and the Nab2 N-terminal domain (Nab2-N). Here, we present a structural and functional analysis of the Gfd1/Nab2-N interaction. Crystallography, supported by solution NMR, shows that Gfd1 residues 126-150 form an alpha-helix when bound to Nab2-N. Engineered Nab2-N and Gfd1 mutants that inhibit this interaction in vitro were used to probe its function in vivo using the genetic interaction between GFD1 and NAB2. Although GFD1 is not essential for viability, its deletion severely impairs growth of rat8-2 (dbp5) cells. Moreover, although Gfd1 overexpression suppresses rat8-2 (dbp5), Gfd1 mutants that do not bind Nab2 only partially suppress rat8-2 (dbp5). Furthermore, rat8-2 (dbp5) cells that express nab2-Y34A, in which binding to Gfd1 is impaired, show a synthetic growth phenotype and nuclear accumulation of poly(A) RNA. These data support the importance of the Gfd1/Nab2 interaction for Dbp5 activity and provide further molecular details of the interactions that facilitate Dbp5-mediated mRNP remodeling in the terminal step of mRNA export.

Structural basis for the function of the Saccharomyces cerevisiae Gfd1 protein in mRNA nuclear export.,Zheng C, Fasken MB, Marshall NJ, Brockmann C, Rubinson ME, Wente SR, Corbett AH, Stewart M J Biol Chem. 2010 Jul 2;285(27):20704-15. Epub 2010 May 12. PMID:20463024^[1]

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

References

↑ Zheng C, Fasken MB, Marshall NJ, Brockmann C, Rubinson ME, Wente SR, Corbett AH, Stewart M. Structural basis for the function of the Saccharomyces cerevisiae Gfd1 protein in mRNA nuclear export. J Biol Chem. 2010 Jul 2;285(27):20704-15. Epub 2010 May 12. PMID:20463024 doi:10.1074/jbc.M110.107276

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/3lcn"

Categories: Large Structures | Saccharomyces cerevisiae | Stewart M

@@ Line 1: / Line 1: @@
 ==Nab2:Gfd1 complex==
-<StructureSection load='3lcn' size='340' side='right' caption='[[3lcn]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='3lcn' size='340' side='right'caption='[[3lcn]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3lcn]] is a 4 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=3LCN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LCN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3lcn]] is a 4 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=3LCN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LCN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2v75|2v75]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NAB2, YGL122C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), GFD1, YM9920.09, YMR255W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=3lcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lcn OCA], [https://pdbe.org/3lcn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lcn RCSB], [https://www.ebi.ac.uk/pdbsum/3lcn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lcn 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=3lcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lcn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lcn RCSB], [http://www.ebi.ac.uk/pdbsum/3lcn PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/NAB2_YEAST NAB2_YEAST] This essential protein binds to polyadenylated RNA and single-stranded DNA. It may be involved not only in RNA processing but also in transcription regulation. Believed to associate directly with nascent RNA polymerase II transcripts and remain associated during subsequent nuclear RNA processing reactions.
 == 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/lc/3lcn_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lc/3lcn_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3lcn ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3lcn" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Stewart, M]]
+[[Category: Stewart M]]
-[[Category: Membrane]]
-[[Category: Metal-binding]]
-[[Category: Mrna transport]]
-[[Category: Nuclear mrna export]]
-[[Category: Nuclear pore complex]]
-[[Category: Nuclear protein]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Protein transport]]
-[[Category: Rna-binding]]
-[[Category: Translocation]]
-[[Category: Transport]]
-[[Category: Zinc-finger]]

3lcn

From Proteopedia

Current revision

Nab2:Gfd1 complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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