9MIR | pdb_00009mir

CryoEM structure of ALK3-ActRIIB bound to BMP6


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


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Literature

CryoEM structure of ALK2:BMP6 reveals distinct mechanism that allow ALK2 to interact with both BMP and activin ligands.

Goebel, E.J.Aykul, S.Hom, W.W.Saotome, K.Economides, A.N.Franklin, M.C.Idone, V.J.

(2025) Proc Natl Acad Sci U S A 122: e2502788122-e2502788122

  • DOI: https://doi.org/10.1073/pnas.2502788122
  • Primary Citation of Related Structures:  
    9MIR, 9N4K

  • PubMed Abstract: 

    Ligands in the transforming growth factor β (TGF-β) family [activins, Bone Morphogenetic Proteins (BMPs), and TGF-βs] signal by bringing together two type I and two type II receptors. Activin receptor-like kinase-2 (ALK2) is the only type I receptor among the seven TGF-β type I receptors that interacts with both activin and BMP ligands. With BMPs, ALK2 acts as a signaling receptor to activate small mothers against decapentaplegic 1 (SMAD1)/5/8 signaling. Alternatively, with activins, such as Activin A (ActA), ALK2 forms nonsignaling complexes that negatively regulate ALK2 and ActA signaling. To gain insight into how ALK2 interacts with two distinct classes of ligands, we resolved the cryoelectron microscopy structure of ALK2 in complex with the type II receptor, ActRIIB, and the ligand, BMP6, in parallel with the corresponding structure with ALK3 for direct comparison. These structures demonstrate that ALK2 and ALK3 utilize different mechanisms to interact with BMP6 at the wrist interface, with ALK2 relying on BMP6 glycosylation and ALK3 relying on a salt bridge. Modeling of ALK2:ActA reveals that binding relies on ActA's fingertip region, mirroring the interaction of ActA with its other receptor, ALK4. Our results demonstrate that ALK2 is a "hybrid" receptor that incorporates features of BMP type I receptors such as ALK3 at the wrist interface and an activin type I receptor such as ALK4 at the fingertip.


  • Organizational Affiliation
    • Connective Tissue Diseases Therapeutic Focus Area, Regeneron Pharmaceuticals, Tarrytown, NY 10591.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
receptor protein serine/threonine kinaseA [auth C],
B [auth D]
145Homo sapiensMutation(s): 0 
Gene Names: Bmpr1a
EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for A0AAQ5BGM0 (Homo sapiens)
Explore A0AAQ5BGM0 
Go to UniProtKB:  A0AAQ5BGM0
GTEx:  ENSG00000107779 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAQ5BGM0
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Bone Morphogenetic Protein 6 (BMP6)C [auth E],
E [auth B]
104Homo sapiensMutation(s): 0 
UniProt
Find proteins for G1RLU5 (Nomascus leucogenys)
Explore G1RLU5 
Go to UniProtKB:  G1RLU5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1RLU5
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ActRIIBD [auth F],
F [auth A]
133Homo sapiensMutation(s): 0 
EC: 2.7.11.30
UniProt
Find proteins for A0A7E6E4Z1 (Phyllostomus discolor)
Explore A0A7E6E4Z1 
Go to UniProtKB:  A0A7E6E4Z1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7E6E4Z1
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, J, K
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I, L
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Data collection, Database references