4N1D

Nodal/BMP2 chimera NB250


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

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
  • Primary Citation of Related Structures:  
    4N1D

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nodal/BMP2 chimera proteinA116Homo sapiensMutation(s): 0 
Gene Names: BMP2BMP2ANODAL
Find proteins for Q96S42 (Homo sapiens)
Explore Q96S42 
Go to UniProtKB:  Q96S42
NIH Common Fund Data Resources
PHAROS  Q96S42
Find proteins for P12643 (Homo sapiens)
Explore P12643 
Go to UniProtKB:  P12643
NIH Common Fund Data Resources
PHAROS  P12643
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.57α = 90
b = 95.57β = 90
c = 97.494γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction
MrBUMPphasing

Structure Validation

View Full Validation Report



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
    Changes: Database references
  • Version 1.2: 2017-07-26
    Changes: Refinement description, Source and taxonomy