4FAO

Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Specificity and Structure of a High Affinity Activin Receptor-like Kinase 1 (ALK1) Signaling Complex.

Townson, S.A.Martinez-Hackert, E.Greppi, C.Lowden, P.Sako, D.Liu, J.Ucran, J.A.Liharska, K.Underwood, K.W.Seehra, J.Kumar, R.Grinberg, A.V.

(2012) J Biol Chem 287: 27313-27325

  • DOI: 10.1074/jbc.M112.377960
  • Primary Citation of Related Structures:  
    4FAO

  • PubMed Abstract: 
  • Activin receptor-like kinase 1 (ALK1), an endothelial cell-specific type I receptor of the TGF-β superfamily, is an important regulator of normal blood vessel development as well as pathological tumor angiogenesis. As such, ALK1 is an important therapeutic target ...

    Activin receptor-like kinase 1 (ALK1), an endothelial cell-specific type I receptor of the TGF-β superfamily, is an important regulator of normal blood vessel development as well as pathological tumor angiogenesis. As such, ALK1 is an important therapeutic target. Thus, several ALK1-directed agents are currently in clinical trials as anti-angiogenic cancer therapeutics. Given the biological and clinical importance of the ALK1 signaling pathway, we sought to elucidate the biophysical and structural basis underlying ALK1 signaling. The TGF-β family ligands BMP9 and BMP10 as well as the three type II TGF-β family receptors ActRIIA, ActRIIB, and BMPRII have been implicated in ALK1 signaling. Here, we provide a kinetic and thermodynamic analysis of BMP9 and BMP10 interactions with ALK1 and type II receptors. Our data show that BMP9 displays a significant discrimination in type II receptor binding, whereas BMP10 does not. We also report the crystal structure of a fully assembled ternary complex of BMP9 with the extracellular domains of ALK1 and ActRIIB. The structure reveals that the high specificity of ALK1 for BMP9/10 is determined by a novel orientation of ALK1 with respect to BMP9, which leads to a unique set of receptor-ligand interactions. In addition, the structure explains how BMP9 discriminates between low and high affinity type II receptors. Taken together, our findings provide structural and mechanistic insights into ALK1 signaling that could serve as a basis for novel anti-angiogenic therapies.


    Organizational Affiliation

    Acceleron Pharma, Cambridge, Massachusetts 02139, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Growth/differentiation factor 2
A, B, G, H, M, N, S, T
110Homo sapiensMutation(s): 0 
Gene Names: BMP9GDF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UK05 (Homo sapiens)
Explore Q9UK05 
Go to UniProtKB:  Q9UK05
PHAROS:  Q9UK05
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase receptor R3
C, D, I, J, O, P, U, V
106Homo sapiensMutation(s): 0 
Gene Names: ACVRL1ACVRLK1ALK1
EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for P37023 (Homo sapiens)
Explore P37023 
Go to UniProtKB:  P37023
PHAROS:  P37023
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Activin receptor type-2B
E, F, K, L, Q, R, W, X
124Homo sapiensMutation(s): 0 
Gene Names: ActRIIBACVR2B
EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for Q13705 (Homo sapiens)
Explore Q13705 
Go to UniProtKB:  Q13705
PHAROS:  Q13705
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth W] , BB [auth X] , CB [auth X] , EB [auth e] , FB [auth e] , HB [auth f] , IB [auth f] , JB [auth k] , 
AB [auth W],  BB [auth X],  CB [auth X],  EB [auth e],  FB [auth e],  HB [auth f],  IB [auth f],  JB [auth k],  KA [auth E],  KB [auth k],  LA [auth E],  MA [auth F],  MB [auth l],  NA [auth F],  NB [auth l],  PA [auth K],  QA [auth K],  SA [auth L],  TA [auth L],  UA [auth Q],  VA [auth Q],  WA [auth R],  XA [auth R],  ZA [auth W]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
DB [auth X], GB [auth e], LB [auth k], OA [auth F], RA [auth K], YA [auth R]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 216.453α = 90
b = 216.453β = 90
c = 216.953γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Database references
  • Version 1.2: 2012-08-29
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary