6MAC

Ternary structure of GDF11 bound to ActRIIB-ECD and Alk5-ECD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural characterization of an activin class ternary receptor complex reveals a third paradigm for receptor specificity.

Goebel, E.J.Corpina, R.A.Hinck, C.S.Czepnik, M.Castonguay, R.Grenha, R.Boisvert, A.Miklossy, G.Fullerton, P.T.Matzuk, M.M.Idone, V.J.Economides, A.N.Kumar, R.Hinck, A.P.Thompson, T.B.

(2019) Proc.Natl.Acad.Sci.USA 116: 15505-15513

  • DOI: 10.1073/pnas.1906253116

  • PubMed Abstract: 
  • TGFβ family ligands, which include the TGFβs, BMPs, and activins, signal by forming a ternary complex with type I and type II receptors. For TGFβs and BMPs, structures of ternary complexes have revealed differences in receptor assembly. However, stru ...

    TGFβ family ligands, which include the TGFβs, BMPs, and activins, signal by forming a ternary complex with type I and type II receptors. For TGFβs and BMPs, structures of ternary complexes have revealed differences in receptor assembly. However, structural information for how activins assemble a ternary receptor complex is lacking. We report the structure of an activin class member, GDF11, in complex with the type II receptor ActRIIB and the type I receptor Alk5. The structure reveals that receptor positioning is similar to the BMP class, with no interreceptor contacts; however, the type I receptor interactions are shifted toward the ligand fingertips and away from the dimer interface. Mutational analysis shows that ligand type I specificity is derived from differences in the fingertips of the ligands that interact with an extended loop specific to Alk4 and Alk5. The study also reveals differences for how TGFβ and GDF11 bind to the same type I receptor, Alk5. For GDF11, additional contacts at the fingertip region substitute for the interreceptor interactions that are seen for TGFβ, indicating that Alk5 binding to GDF11 is more dependent on direct contacts. In support, we show that a single residue of Alk5 (Phe 84 ), when mutated, abolishes GDF11 signaling, but has little impact on TGFβ signaling. The structure of GDF11/ActRIIB/Alk5 shows that, across the TGFβ family, different mechanisms regulate type I receptor binding and specificity, providing a molecular explanation for how the activin class accommodates low-affinity type I interactions without the requirement of cooperative receptor interactions.


    Organizational Affiliation

    Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030.,Skeletal Diseases Therapeutic Focus Area, Regeneron Pharmaceuticals, Tarrytown, NY 10591.,Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, Cincinnati, OH 45267; tom.thompson@uc.edu.,Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, Cincinnati, OH 45267.,Discovery Group, Acceleron Pharma, Cambridge, MA 02139.,Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Growth/differentiation factor 11
A
108Homo sapiensMutation(s): 0 
Gene Names: GDF11 (BMP11)
Find proteins for O95390 (Homo sapiens)
Go to Gene View: GDF11
Go to UniProtKB:  O95390
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Activin receptor type-2B
C
95Rattus norvegicusMutation(s): 0 
Gene Names: Acvr2b (Actriib)
EC: 2.7.11.30
Find proteins for P38445 (Rattus norvegicus)
Go to UniProtKB:  P38445
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
TGF-beta receptor type-1
K
80Homo sapiensMutation(s): 0 
Gene Names: TGFBR1 (ALK5, SKR4)
EC: 2.7.11.30
Find proteins for P36897 (Homo sapiens)
Go to Gene View: TGFBR1
Go to UniProtKB:  P36897
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.222 
  • Space Group: P 32 1 2
Unit Cell:
Length (Å)Angle (°)
a = 116.624α = 90.00
b = 116.624β = 90.00
c = 56.625γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
DIALSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-07-31
    Type: Data collection, Database references
  • Version 1.2: 2019-08-14
    Type: Data collection, Database references