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 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 U S A 116: 15505-15513

  • DOI: 10.1073/pnas.1906253116
  • Primary Citation of Related Structures:  
    6MAC

  • 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, structur ...

    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 Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, Cincinnati, OH 45267; tom.thompson@uc.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Growth/differentiation factor 11 A108Homo sapiensMutation(s): 0 
Gene Names: GDF11BMP11
Find proteins for O95390 (Homo sapiens)
Explore O95390 
Go to UniProtKB:  O95390
NIH Common Fund Data Resources
PHAROS:  O95390
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Activin receptor type-2B C95Rattus norvegicusMutation(s): 0 
Gene Names: Acvr2bActriib
EC: 2.7.11.30
Find proteins for P38445 (Rattus norvegicus)
Explore P38445 
Go to UniProtKB:  P38445
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
TGF-beta receptor type-1 K80Homo sapiensMutation(s): 0 
Gene Names: TGFBR1ALK5SKR4
EC: 2.7.11.30
Find proteins for P36897 (Homo sapiens)
Explore P36897 
Go to UniProtKB:  P36897
NIH Common Fund Data Resources
PHAROS:  P36897
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C
2-acetamido-2-deoxy-beta-D-glucopyranose
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 
  • R-Value Observed: 0.226 
  • Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.624α = 90
b = 116.624β = 90
c = 56.625γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary