NMR structure of Npm1_c70

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 400 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

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This is version 1.2 of the entry. See complete history


Structure of Nucleophosmin DNA-binding Domain and Analysis of Its Complex with a G-quadruplex Sequence from the c-MYC Promoter.

Gallo, A.Lo Sterzo, C.Mori, M.Di Matteo, A.Bertini, I.Banci, L.Brunori, M.Federici, L.

(2012) J Biol Chem 287: 26539-26548

  • DOI: https://doi.org/10.1074/jbc.M112.371013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Nucleophosmin (NPM1) is a nucleocytoplasmic shuttling protein, mainly localized at nucleoli, that plays a key role in several cellular functions, including ribosome maturation and export, centrosome duplication, and response to stress stimuli. More than 50 mutations at the terminal exon of the NPM1 gene have been identified so far in acute myeloid leukemia; the mutated proteins are aberrantly and stably localized in the cytoplasm due to high destabilization of the NPM1 C-terminal domain and the appearance of a new nuclear export signal. We have shown previously that the 70-residue NPM1 C-terminal domain (NPM1-C70) is able to bind with high affinity a specific region at the c-MYC gene promoter characterized by parallel G-quadruplex structure. Here we present the solution structure of the NPM1-C70 domain and NMR analysis of its interaction with a c-MYC-derived G-quadruplex. These data were used to calculate an experimentally restrained molecular docking model for the complex. The NPM1-C70 terminal three-helix bundle binds the G-quadruplex DNA at the interface between helices H1 and H2 through electrostatic interactions with the G-quadruplex phosphate backbone. Furthermore, we show that the 17-residue lysine-rich sequence at the N terminus of the three-helix bundle is disordered and, although necessary, does not participate directly in the contact surface in the complex.

  • Organizational Affiliation

    Magnetic Resonance Center, Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleophosmin74Homo sapiensMutation(s): 0 
Gene Names: NPM1NPM
UniProt & NIH Common Fund Data Resources
Find proteins for P06748 (Homo sapiens)
Explore P06748 
Go to UniProtKB:  P06748
PHAROS:  P06748
GTEx:  ENSG00000181163 
Entity Groups  
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UniProt GroupP06748
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 400 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2012-08-22
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Data collection, Database references, Other