Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5.05 kDa 
• Atom Count: 350 
• Modelled Residue Count: 41 
• Deposited Residue Count: 41 
• Unique protein chains: 1

2NAB

Nizp1-C2HR zinc finger structure

• PDB DOI: 10.2210/pdb2NAB/pdb
• BMRB: 25934

• Classification: TRANSCRIPTION
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-12-22 Released: 2016-03-09 
• Deposition Author(s): Berardi, A., Quilici, G., Spiliotopoulos, D., Corral-Rodriguez, M., Martin, F., Degano, M., Tonon, G., Musco, G.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Literature

Structural basis for PHDVC5HCHNSD1-C2HRNizp1 interaction: implications for Sotos syndrome.

Berardi, A., Quilici, G., Spiliotopoulos, D., Corral-Rodriguez, M.A., Martin-Garcia, F., Degano, M., Tonon, G., Ghitti, M., Musco, G.

(2016) Nucleic Acids Res 44: 3448-3463

• PubMed: 26896805 
• DOI: 10.1093/nar/gkw103
• Primary Citation of Related Structures:  
  2NAA, 2NAB


• PubMed Abstract: 
  

Sotos syndrome is an overgrowth syndrome caused by mutations within the functional domains ofNSD1 gene coding for NSD1, a multidomain protein regulating chromatin structure and gene expression. In particular, PHDVC5HCHNSD1 tandem domain, composed by a classical (PHDV) and an atypical (C5HCH) plant homeo-domain (PHD) finger, is target of several pathological missense-mutations. PHDVC5HCHNSD1 is also crucial for NSD1-dependent transcriptional regulation and interacts with the C2HR domain of transcriptional repressor Nizp1 (C2HRNizp1)in vitro To get molecular insights into the mechanisms dictating the patho-physiological relevance of the PHD finger tandem domain, we solved its solution structure and provided a structural rationale for the effects of seven Sotos syndrome point-mutations. To investigate PHDVC5HCHNSD1 role as structural platform for multiple interactions, we characterized its binding to histone H3 peptides and to C2HRNizp1 by ITC and NMR. We observed only very weak electrostatic interactions with histone H3 N-terminal tails, conversely we proved specific binding to C2HRNizp1 We solved C2HRNizp1 solution structure and generated a 3D model of the complex, corroborated by site-directed mutagenesis. We suggest a mechanistic scenario where NSD1 interactions with cofactors such as Nizp1 are impaired by PHDVC5HCHNSD1 pathological mutations, thus impacting on the repression of growth-promoting genes, leading to overgrowth conditions.

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Organizational Affiliation: 

Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger protein 496	A	41	Mus musculus	Mutation(s): 0  Gene Names: Znf496, Nizp11, Zfp496, Zkscan17
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SXI5 (Mus musculus) Explore Q5SXI5  Go to UniProtKB:  Q5SXI5
IMPC:  MGI:2679270

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2NAB Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-12-22 
• Released Date: 2016-03-09 
Deposition Author(s): Berardi, A., Quilici, G., Spiliotopoulos, D., Corral-Rodriguez, M., Martin, F., Degano, M., Tonon, G., Musco, G.

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2016-05-04
  Changes: Database references