2fv2: Difference between revisions

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New page: left|200px<br /> <applet load="2fv2" size="450" color="white" frame="true" align="right" spinBox="true" caption="2fv2, resolution 2.20Å" /> '''Crystal Structure A...
 
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[[Image:2fv2.gif|left|200px]]<br />
<applet load="2fv2" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2fv2, resolution 2.20&Aring;" />
'''Crystal Structure Analysis of human Rcd-1 conserved region'''<br />


==Overview==
==Crystal Structure Analysis of human Rcd-1 conserved region==
Rcd-1, a protein highly conserved across eukaryotes, was initially, identified as a factor essential for nitrogen starvation-invoked, differentiation in fission yeast, and its Saccharomyces cerevisiae, homolog, CAF40, has been identified as part of the CCR4-NOT transcription, complex, where it interacts with the NOT1 protein. Mammalian homologs are, involved in various cellular differentiation processes including retinoic, acid-induced differentiation and hematopoetic cell development. Here, we, present the 2.2 A X-ray structure of the highly conserved region of human, Rcd-1 and investigate possible functional abilities of this and the, full-length protein. The monomer is made up of six armadillo repeats, forming a solvent-accessible, positively-charged cleft 21-22 A wide that, in contrast to other armadillo proteins, stays fully exposed in the dimer., Prompted by this finding, we established that Rcd-1 can bind to single-, and double-stranded oligonucleotides in vitro with the affinity of G/C/T, &gt;&gt; A. Mutation of an arginine residue within the cleft strongly reduced or, abolished oligonucleotide binding. Rcd-1's ability to bind to nucleic, acids, in addition to the previously reported protein-protein interaction, with NOT1, suggests a new feature in Rcd-1's role in regulation of overall, cellular differentiation processes.
<StructureSection load='2fv2' size='340' side='right'caption='[[2fv2]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[2fv2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FV2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FV2 FirstGlance]. <br>
2FV2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with MN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2FV2 OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fv2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fv2 OCA], [https://pdbe.org/2fv2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fv2 RCSB], [https://www.ebi.ac.uk/pdbsum/2fv2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fv2 ProSAT]</span></td></tr>
Atomic model of human Rcd-1 reveals an armadillo-like-repeat protein with in vitro nucleic acid binding properties., Garces RG, Gillon W, Pai EF, Protein Sci. 2007 Feb;16(2):176-88. Epub 2006 Dec 22. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17189474 17189474]
</table>
== Function ==
[https://www.uniprot.org/uniprot/CNOT9_HUMAN CNOT9_HUMAN] Component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation. Additional complex functions may be a consequence of its influence on mRNA expression. Involved in down-regulation of MYB- and JUN-dependent transcription. May play a role in cell differentiation (By similarity). Can bind oligonucleotides, such as poly-G, poly-C or poly-T (in vitro), but the physiological relevance of this is not certain. Does not bind poly-A. Enhances ligand-dependent transcriptional activity of nuclear hormone receptors, including RARA, expect ESR1-mediated transcription that is not only slightly increased, if at all.<ref>PMID:17189474</ref> <ref>PMID:18180299</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/fv/2fv2_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/main_output.php?pdb_ID=2fv2 ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Garces, R.G.]]
[[Category: Garces RG]]
[[Category: Gillon, W.]]
[[Category: Gillon W]]
[[Category: Pai, E.F.]]
[[Category: Pai EF]]
[[Category: MN]]
[[Category: armadillo-repeat]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 22:10:40 2007''

Latest revision as of 12:25, 14 February 2024

Crystal Structure Analysis of human Rcd-1 conserved regionCrystal Structure Analysis of human Rcd-1 conserved region

Structural highlights

2fv2 is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CNOT9_HUMAN Component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation. Additional complex functions may be a consequence of its influence on mRNA expression. Involved in down-regulation of MYB- and JUN-dependent transcription. May play a role in cell differentiation (By similarity). Can bind oligonucleotides, such as poly-G, poly-C or poly-T (in vitro), but the physiological relevance of this is not certain. Does not bind poly-A. Enhances ligand-dependent transcriptional activity of nuclear hormone receptors, including RARA, expect ESR1-mediated transcription that is not only slightly increased, if at all.[1] [2]

Evolutionary Conservation

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

References

  1. ↑ Garces RG, Gillon W, Pai EF. Atomic model of human Rcd-1 reveals an armadillo-like-repeat protein with in vitro nucleic acid binding properties. Protein Sci. 2007 Feb;16(2):176-88. Epub 2006 Dec 22. PMID:17189474 doi:10.1110/ps.062600507
  2. ↑ Garapaty S, Mahajan MA, Samuels HH. Components of the CCR4-NOT complex function as nuclear hormone receptor coactivators via association with the NRC-interacting Factor NIF-1. J Biol Chem. 2008 Mar 14;283(11):6806-16. doi: 10.1074/jbc.M706986200. Epub 2008 , Jan 7. PMID:18180299 doi:http://dx.doi.org/10.1074/jbc.M706986200

2fv2, resolution 2.20Å

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