View source for 1rkj


==Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target==
<StructureSection load='1rkj' size='340' side='right'caption='[[1rkj]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1rkj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesocricetus_auratus Mesocricetus auratus] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RKJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RKJ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1rkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkj OCA], [https://pdbe.org/1rkj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rkj RCSB], [https://www.ebi.ac.uk/pdbsum/1rkj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rkj ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NUCL_MESAU NUCL_MESAU] Nucleolin is the major nucleolar protein of growing eukaryotic cells. It is found associated with intranucleolar chromatin and pre-ribosomal particles. It induces chromatin decondensation by binding to histone H1. It is thought to play a role in pre-rRNA transcription and ribosome assembly. May play a role in the process of transcriptional elongation. Binds RNA oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the telomeric single-stranded DNA 5'-TTAGGG-3' repeats (By similarity).<ref>PMID:3409881</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/rk/1rkj_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=1rkj ConSurf].
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== Publication Abstract from PubMed ==
Nucleolin is a 70 kDa multidomain protein involved in several steps of eukaryotic ribosome biogenesis. In vitro selection in combination with mutagenesis and structural analysis identified binding sites in pre-rRNA with the consensus (U/G)CCCG(A/G) in the context of a hairpin structure, the nucleolin recognition element (NRE). The central region of the protein contains four tandem RNA-binding domains (RBDs), of which the first two are responsible for the RNA-binding specificity and affinity for NREs. Here, we present the solution structure of the 28 kDa complex formed by the two N-terminal RNA-binding domains of nucleolin (RBD12) and a natural pre-rRNA target, b2NRE. The structure demonstrates that the sequence-specific recognition of the pre-rRNA NRE is achieved by intermolecular hydrogen bonds and stacking interactions involving mainly the beta-sheet surfaces of the two RBDs and the linker residues. A comparison with our previously determined NMR structure of RBD12 in complex with an in vitro selected RNA target, sNRE, shows that although the sequence-specific recognition of the loop consensus nucleotides is the same in the two complexes, they differ in several aspects. While the protein makes numerous specific contacts to the non-consensus nucleotides in the loop E motif (S-turn) in the upper part of the sNRE stem, nucleolin RBD12 contacts only consensus nucleotides in b2NRE. The absence of these upper stem contacts from the RBD12/b2NRE complex results in a much less stable complex, as demonstrated by kinetic analyses. The role of the loop E motif in high-affinity binding is supported by gel-shift analyses with a series of sNRE mutants. The less stable interaction of RBD12 with the natural RNA target is consistent with the proposed role of nucleolin as a chaperone that interacts transiently with pre-rRNA to prevent misfolding.

Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target.,Johansson C, Finger LD, Trantirek L, Mueller TD, Kim S, Laird-Offringa IA, Feigon J J Mol Biol. 2004 Apr 2;337(4):799-816. PMID:15033352<ref>PMID:15033352</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 1rkj" style="background-color:#fffaf0;"></div>

==See Also==
*[[Nucleolin|Nucleolin]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Mesocricetus auratus]]
[[Category: Mus musculus]]
[[Category: Feigon J]]
[[Category: Finger LD]]
[[Category: Johansson C]]
[[Category: Kim S]]
[[Category: Laird-Offringa IA]]
[[Category: Mueller TD]]
[[Category: Trantirek L]]