Biological Assembly 1  

 3D View: Structure

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.51 kDa 
• Atom Count: 568 
• Modelled Residue Count: 70 
• Deposited Residue Count: 74 
• Unique protein chains: 1

2LLH

NMR structure of Npm1_c70

• DOI: 10.2210/pdb2LLH/pdb
• BMRB: 18048

• Classification: DNA BINDING PROTEIN, CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-11-09 Released: 2012-06-27 
• Deposition Author(s): Banci, L., Bertini, I., Brunori, M., Di Matteo, A., Federici, L., Gallo, A., Lo Sterzo, C., Mori, M.

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Experimental Data Snapshot

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

Literature

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

• PubMed: 22707729 
• DOI: 10.1074/jbc.M112.371013
• Primary Citation of Related Structures:  
  2LLH


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleophosmin	A	74	Homo sapiens	Mutation(s): 0  Gene Names: NPM1, NPM
Find proteins for P06748 (Homo sapiens) Explore P06748  Go to UniProtKB:  P06748
NIH Common Fund Data Resources
PHAROS:  P06748 GTEx:  ENSG00000181163

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 400 
• Conformers Submitted: 20 
• Selection Criteria: target function 
• OLDERADO: 2LLH Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-11-09 
• Released Date: 2012-06-27 
Deposition Author(s): Banci, L., Bertini, I., Brunori, M., Di Matteo, A., Federici, L., Gallo, A., Lo Sterzo, C., Mori, M.

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 1.1: 2012-08-22
  Changes: Database references