1rkj
From Proteopedia
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|PDB= 1rkj |SIZE=350|CAPTION= <scene name='initialview01'>1rkj</scene> | |PDB= 1rkj |SIZE=350|CAPTION= <scene name='initialview01'>1rkj</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= NCL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10036 Mesocricetus auratus]) | |GENE= NCL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10036 Mesocricetus auratus]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1fje|1FJE]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkj OCA], [http://www.ebi.ac.uk/pdbsum/1rkj PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rkj RCSB]</span> | ||
}} | }} | ||
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[[Category: rbd]] | [[Category: rbd]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:29:28 2008'' |
Revision as of 20:29, 30 March 2008
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| Ligands: | , , , | ||||||
| Gene: | NCL (Mesocricetus auratus) | ||||||
| Related: | 1FJE
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target
Overview
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.
About this Structure
1RKJ is a Single protein structure of sequence from Mesocricetus auratus. Full crystallographic information is available from OCA.
Reference
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
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