4X1J

X-ray crystal structure of the dimeric BMP antagonist NBL1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of Neuroblastoma Suppressor of Tumorigenicity 1 (NBL1): INSIGHTS FOR THE FUNCTIONAL VARIABILITY ACROSS BONE MORPHOGENETIC PROTEIN (BMP) ANTAGONISTS.

Nolan, K.Kattamuri, C.Luedeke, D.M.Angerman, E.B.Rankin, S.A.Stevens, M.L.Zorn, A.M.Thompson, T.B.

(2015) J.Biol.Chem. 290: 4759-4771

  • DOI: 10.1074/jbc.M114.628412

  • PubMed Abstract: 
  • Bone morphogenetic proteins (BMPs) are antagonized through the action of numerous extracellular protein antagonists, including members from the differential screening-selected gene aberrative in neuroblastoma (DAN) family. In vivo, misregulation of t ...

    Bone morphogenetic proteins (BMPs) are antagonized through the action of numerous extracellular protein antagonists, including members from the differential screening-selected gene aberrative in neuroblastoma (DAN) family. In vivo, misregulation of the balance between BMP signaling and DAN inhibition can lead to numerous disease states, including cancer, kidney nephropathy, and pulmonary arterial hypertension. Despite this importance, very little information is available describing how DAN family proteins effectively inhibit BMP ligands. Furthermore, our understanding for how differences in individual DAN family members arise, including affinity and specificity, remains underdeveloped. Here, we present the structure of the founding member of the DAN family, neuroblastoma suppressor of tumorigenicity 1 (NBL1). Comparing NBL1 to the structure of protein related to Dan and Cerberus (PRDC), a more potent BMP antagonist within the DAN family, a number of differences were identified. Through a mutagenesis-based approach, we were able to correlate the BMP binding epitope in NBL1 with that in PRDC, where introduction of specific PRDC amino acids in NBL1 (A58F and S67Y) correlated with a gain-of-function inhibition toward BMP2 and BMP7, but not GDF5. Although NBL1(S67Y) was able to antagonize BMP7 as effectively as PRDC, NBL1(S67Y) was still 32-fold weaker than PRDC against BMP2. Taken together, this data suggests that alterations in the BMP binding epitope can partially account for differences in the potency of BMP inhibition within the DAN family.


    Organizational Affiliation

    From the Department of Molecular Genetics, Biochemistry, and Microbiology, The University of Cincinnati, Cincinnati, Ohio 45267 and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neuroblastoma suppressor of tumorigenicity 1
A, B
116Homo sapiensMutation(s): 0 
Gene Names: NBL1 (DAN, DAND1)
Find proteins for P41271 (Homo sapiens)
Go to Gene View: NBL1
Go to UniProtKB:  P41271
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.216 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.665α = 90.00
b = 59.665β = 90.00
c = 145.018γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM38060

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-02-18
    Type: Database references
  • Version 1.2: 2015-03-04
    Type: Database references
  • Version 1.3: 2016-08-17
    Type: Structure summary
  • Version 1.4: 2017-09-20
    Type: Author supporting evidence, Derived calculations