1rkj

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[[Image:1rkj.gif|left|200px]]
 
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==Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target==
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The line below this paragraph, containing "STRUCTURE_1rkj", creates the "Structure Box" on the page.
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<StructureSection load='1rkj' size='340' side='right'caption='[[1rkj]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<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>
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{{STRUCTURE_1rkj| PDB=1rkj | SCENE= }}
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rk/1rkj_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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'''Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target'''
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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>
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==Overview==
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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.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1RKJ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mesocricetus_auratus Mesocricetus auratus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RKJ OCA].
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</div>
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<div class="pdbe-citations 1rkj" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/15033352 15033352]
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*[[Nucleolin|Nucleolin]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Mesocricetus auratus]]
[[Category: Mesocricetus auratus]]
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[[Category: Single protein]]
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[[Category: Mus musculus]]
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[[Category: Feigon, J.]]
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[[Category: Feigon J]]
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[[Category: Finger, L D.]]
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[[Category: Finger LD]]
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[[Category: Johansson, C.]]
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[[Category: Johansson C]]
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[[Category: Kim, S.]]
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[[Category: Kim S]]
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[[Category: Laird-Offringa, I A.]]
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[[Category: Laird-Offringa IA]]
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[[Category: Mueller, T D.]]
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[[Category: Mueller TD]]
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[[Category: Trantirek, L.]]
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[[Category: Trantirek L]]
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[[Category: Protein-rna complex]]
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[[Category: Rbd]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 07:36:38 2008''
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Current revision

Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target

PDB ID 1rkj

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