3Q4T

Crystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with dorsomorphin

• PDB DOI:  https://doi.org/10.2210/pdb3Q4T/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2010-12-24 Released: 2011-02-09 
• Deposition Author(s): Chaikuad, A., Alfano, I., Mahajan, P., Cooper, C.D.O., Sanvitale, C., Vollmar, M., Krojer, T., Muniz, J.R.C., Raynor, J., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.223 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 

Literature

Small Molecules Dorsomorphin and LDN-193189 Inhibit Myostatin/GDF8 Signaling and Promote Functional Myoblast Differentiation.

Horbelt, D., Boergermann, J.H., Chaikuad, A., Alfano, I., Williams, E., Lukonin, I., Timmel, T., Bullock, A.N., Knaus, P.

(2015) J Biol Chem 290: 3390-3404

• PubMed: 25368322 
• DOI: https://doi.org/10.1074/jbc.M114.604397
• Primary Citation of Related Structures:  
  3Q4T


• PubMed Abstract: 
  

GDF8, or myostatin, is a member of the TGF-β superfamily of secreted polypeptide growth factors. GDF8 is a potent negative regulator of myogenesis both in vivo and in vitro. We found that GDF8 signaling was inhibited by the small molecule ATP competitive inhibitors dorsomorphin and LDN-193189. These compounds were previously shown to be potent inhibitors of BMP signaling by binding to the BMP type I receptors ALK1/2/3/6. We present the crystal structure of the type II receptor ActRIIA with dorsomorphin and demonstrate that dorsomorphin or LDN-193189 target GDF8 induced Smad2/3 signaling and repression of myogenic transcription factors. As a result, both inhibitors rescued myogenesis in myoblasts treated with GDF8. As revealed by quantitative live cell microscopy, treatment with dorsomorphin or LDN-193189 promoted the contractile activity of myotubular networks in vitro. We therefore suggest these inhibitors as suitable tools to promote functional myogenesis.

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Organizational Affiliation: 

From the Institute for Chemistry-Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany, [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 75.78 kDa 
• Atom Count: 5,572 
• Modelled Residue Count: 613 
• Deposited Residue Count: 644 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Activin receptor type-2A	A, B	322	Homo sapiens	Mutation(s): 0  Gene Names: ACVR2, ACVR2A EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for P27037 (Homo sapiens) Explore P27037  Go to UniProtKB:  P27037
PHAROS:  P27037

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TAK	C [auth A], Q [auth B]	6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine C24 H25 N5 O XHBVYDAKJHETMP-UHFFFAOYSA-N
PG4	P [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], R [auth B], S [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	AA [auth B], BA [auth B], CA [auth B], DA [auth B], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.223 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.1	α = 90
b = 110.1	β = 90
c = 206.911	γ = 120

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-09 
Deposition Author(s): Chaikuad, A., Alfano, I., Mahajan, P., Cooper, C.D.O., Sanvitale, C., Vollmar, M., Krojer, T., Muniz, J.R.C., Raynor, J., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2011-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-12-10
  Changes: Database references
• Version 1.3: 2015-02-25
  Changes: Database references
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description