Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.92 kDa 
• Atom Count: 3660 
• Modelled Residue Count: 419 
• Deposited Residue Count: 439 
• Unique protein chains: 2

3H9R

Crystal structure of the kinase domain of type I activin receptor (ACVR1) in complex with FKBP12 and dorsomorphin

• PDB DOI: 10.2210/pdb3H9R/pdb

• Classification: ISOMERASE/PROTEIN KINASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus, Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-30 Released: 2009-06-02 
• Deposition Author(s): Chaikuad, A., Alfano, I., Shrestha, B., Muniz, J.R.C., Petrie, K., Fedorov, O., Phillips, C., Bishop, S., Mahajan, P., Pike, A.C.W., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S., Bullock, A., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.256 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Literature

Structure of the Bone Morphogenetic Protein Receptor ALK2 and Implications for Fibrodysplasia Ossificans Progressiva.

Chaikuad, A., Alfano, I., Kerr, G., Sanvitale, C.E., Boergermann, J.H., Triffitt, J.T., von Delft, F., Knapp, S., Knaus, P., Bullock, A.N.

(2012) J Biol Chem 287: 36990-36998

• PubMed: 22977237 
• DOI: 10.1074/jbc.M112.365932
• Primary Citation of Related Structures:  
  3H9R


• PubMed Abstract: 
  

Bone morphogenetic protein (BMP) receptor kinases are tightly regulated to control development and tissue homeostasis. Mutant receptor kinase domains escape regulation leading to severely degenerative diseases and represent an important therapeutic target. Fibrodysplasia ossificans progressiva (FOP) is a rare but devastating disorder of extraskeletal bone formation. FOP-associated mutations in the BMP receptor ALK2 reduce binding of the inhibitor FKBP12 and promote leaky signaling in the absence of ligand. To establish structural mechanisms of receptor regulation and to address the effects of FOP mutation, we determined the crystal structure of the cytoplasmic domain of ALK2 in complex with the inhibitors FKBP12 and dorsomorphin. FOP mutations break critical interactions that stabilize the inactive state of the kinase, thereby facilitating structural rearrangements that diminish FKBP12 binding and promote the correct positioning of the glycine-serine-rich loop and αC helix for kinase activation. The balance of these effects accounts for the comparable activity of R206H and L196P. Kinase activation in the clinically benign mutant L196P is far weaker than R206H but yields equivalent signals due to the stronger interaction of FKBP12 with R206H. The presented ALK2 structure offers a valuable template for the further design of specific inhibitors of BMP signaling.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Activin receptor type-1	A	330	Homo sapiens	Mutation(s): 0  Gene Names: ACVR1, ACVRLK2 EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for Q04771 (Homo sapiens) Explore Q04771  Go to UniProtKB:  Q04771
PHAROS:  Q04771 GTEx:  ENSG00000115170

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1A	B	109	Homo sapiens	Mutation(s): 0  Gene Names: FKBP1, FKBP12, FKBP1A EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62942 (Homo sapiens) Explore P62942  Go to UniProtKB:  P62942
PHAROS:  P62942 GTEx:  ENSG00000088832

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TAK	C [auth A]	6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine C24 H25 N5 O XHBVYDAKJHETMP-UHFFFAOYSA-N
PG4	I [auth A], J [auth A], K [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
TAK	BindingDB:  3H9R	IC50: min: 9.76, max: 148.1 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.256 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.349	α = 90
b = 62.345	β = 90
c = 171.597	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-04-30 
• Released Date: 2009-06-02 
Deposition Author(s): Chaikuad, A., Alfano, I., Shrestha, B., Muniz, J.R.C., Petrie, K., Fedorov, O., Phillips, C., Bishop, S., Mahajan, P., Pike, A.C.W., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S., Bullock, A., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2012-11-28
  Changes: Database references