4N1D

Nodal/BMP2 chimera NB250


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.912 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Designer Nodal/BMP2 Chimeras Mimic Nodal Signaling, Promote Chondrogenesis, and Reveal a BMP2-like Structure.

Esquivies, L.Blackler, A.Peran, M.Rodriguez-Esteban, C.Izpisua Belmonte, J.C.Booker, E.Gray, P.C.Ahn, C.Kwiatkowski, W.Choe, S.

(2014) J.Biol.Chem. 289: 1788-1797

  • DOI: 10.1074/jbc.M113.529180

  • PubMed Abstract: 
  • Nodal, a member of the TGF-β superfamily, plays an important role in vertebrate and invertebrate early development. The biochemical study of Nodal and its signaling pathway has been a challenge, mainly because of difficulties in producing the protein ...

    Nodal, a member of the TGF-β superfamily, plays an important role in vertebrate and invertebrate early development. The biochemical study of Nodal and its signaling pathway has been a challenge, mainly because of difficulties in producing the protein in sufficient quantities. We have developed a library of stable, chemically refoldable Nodal/BMP2 chimeric ligands (NB2 library). Three chimeras, named NB250, NB260, and NB264, show Nodal-like signaling properties including dependence on the co-receptor Cripto and activation of the Smad2 pathway. NB250, like Nodal, alters heart looping during the establishment of embryonic left-right asymmetry, and both NB250 and NB260, as well as Nodal, induce chondrogenic differentiation of human adipose-derived stem cells. This Nodal-induced differentiation is shown to be more efficient than BPM2-induced differentiation. Interestingly, the crystal structure of NB250 shows a backbone scaffold similar to that of BMP2. Our results show that these chimeric ligands may have therapeutic implications in cartilage injuries.


    Organizational Affiliation

    From the Structural Biology Laboratory.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nodal/BMP2 chimera protein
A
116Homo sapiensMutation(s): 0 
Gene Names: BMP2 (BMP2A), NODAL
Find proteins for P12643 (Homo sapiens)
Go to Gene View: BMP2
Go to UniProtKB:  P12643
Find proteins for Q96S42 (Homo sapiens)
Go to Gene View: NODAL
Go to UniProtKB:  Q96S42
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.912 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.175 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 95.570α = 90.00
b = 95.570β = 90.00
c = 97.494γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Blu-Icedata collection
PHENIXrefinement
XDSdata reduction
MrBUMPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-10-04 
  • Released Date: 2013-12-04 
  • Deposition Author(s): Esquivies, L.

Revision History 

  • Version 1.0: 2013-12-04
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Database references
  • Version 1.2: 2017-07-26
    Type: Refinement description, Source and taxonomy