7OLY

Structure of activin A in complex with an ActRIIB-Alk4 fusion reveal insight into activin receptor interactions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structures of activin ligand traps using natural sets of type I and type II TGF beta receptors.

Goebel, E.J.Kattamuri, C.Gipson, G.R.Krishnan, L.Chavez, M.Czepnik, M.Maguire, M.C.Grenha, R.Hakansson, M.Logan, D.T.Grinberg, A.V.Sako, D.Castonguay, R.Kumar, R.Thompson, T.B.

(2022) iScience 25: 103590-103590

  • DOI: https://doi.org/10.1016/j.isci.2021.103590
  • Primary Citation of Related Structures:  
    7MRZ, 7OLY

  • PubMed Abstract: 

    The 30+ unique ligands of the TGFβ family signal by forming complexes using different combinations of type I and type II receptors. Therapeutically, the extracellular domain of a single receptor fused to an Fc molecule can effectively neutralize subsets of ligands. Increased ligand specificity can be accomplished by using the extracellular domains of both the type I and type II receptor to mimic the naturally occurring signaling complex. Here, we report the structure of one "type II-type I-Fc" fusion, ActRIIB-Alk4-Fc, in complex with two TGFβ family ligands, ActA, and GDF11, providing a snapshot of this therapeutic platform. The study reveals that extensive contacts are formed by both receptors, replicating the ternary signaling complex, despite the inherent low affinity of Alk4. Our study shows that low-affinity type I interactions support altered ligand specificity and can be visualized at the molecular level using this platform.


  • Organizational Affiliation

    Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, 231 Albert Sabin Way ML 0524, Cincinnati, OH 45267, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inhibin beta A chain116Homo sapiensMutation(s): 0 
Gene Names: INHBA
UniProt & NIH Common Fund Data Resources
Find proteins for P08476 (Homo sapiens)
Explore P08476 
Go to UniProtKB:  P08476
PHAROS:  P08476
GTEx:  ENSG00000122641 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08476
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Activin receptor type-2BB [auth C]133Homo sapiensMutation(s): 0 
Gene Names: ACVR2B
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
GTEx:  ENSG00000114739 
Entity Groups  
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UniProt GroupQ13705
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q13705-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab heavy chainC [auth H]225Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Activin receptor type-1BD [auth K]121Homo sapiensMutation(s): 0 
Gene Names: ACVR1BACVRLK4ALK4
EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for P36896 (Homo sapiens)
Explore P36896 
Go to UniProtKB:  P36896
PHAROS:  P36896
GTEx:  ENSG00000135503 
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UniProt GroupP36896
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Fab light chainE [auth L]221Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth B]6N-Glycosylation
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.375α = 90
b = 68.375β = 90
c = 975.538γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MxCuBEdata collection
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-23
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary