Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26.05 kDa 
• Atom Count: 1,804 
• Modelled Residue Count: 196 
• Deposited Residue Count: 196 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 1RKJ

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

• PDB DOI: 10.2210/pdb1RKJ/pdb
• NDB: 1RKJ
• BMRB: 4867

• Classification: Transcription/RNA
• Organism(s): Mesocricetus auratus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-11-21 Released: 2004-04-27 
• Deposition Author(s): Johansson, C., Finger, L.D., Trantirek, L., Mueller, T.D., Kim, S., Laird-Offringa, I.A., Feigon, J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 40 
• Conformers Submitted: 14 
• Selection Criteria: structures with the lowest energy 

Literature

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

Johansson, C., Finger, L.D., Trantirek, L., Mueller, T.D., Kim, S., Laird-Offringa, I.A., Feigon, J.

(2004) J Mol Biol 337: 799-816

• PubMed: 15033352 
• DOI: 10.1016/j.jmb.2004.01.056
• Primary Citation of Related Structures:  
  1RKJ


• PubMed Abstract: 
  

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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Organizational Affiliation: 

Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California, Los Angeles, CA 90095-1569, USA.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleolin	B [auth A]	175	Mesocricetus auratus	Mutation(s): 0  Gene Names: NCL
UniProt
Find proteins for P08199 (Mesocricetus auratus) Explore P08199  Go to UniProtKB:  P08199

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*AP*UP*GP*CP*CP*UP*CP*CP*CP*GP*AP*GP*UP*GP*CP*AP*UP*CP*C)-3'	A [auth B]	21	N/A

Small Molecules

Binding Affinity Annotations
ID	Source	Binding Affinity
RNA	PDBBind:  1RKJ	Kd: 1100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 40 
• Conformers Submitted: 14 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-27 
Deposition Author(s): Johansson, C., Finger, L.D., Trantirek, L., Mueller, T.D., Kim, S., Laird-Offringa, I.A., Feigon, J.

Revision History  

• Version 1.0: 2004-04-27
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-02
  Changes: Data collection, Database references, Derived calculations