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- PDB-9n4k: CryoEM structure of ALK2-ActRIIB bound to BMP6 -

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Basic information

Entry
Database: PDB / ID: 9n4k
TitleCryoEM structure of ALK2-ActRIIB bound to BMP6
Components
  • (Activin receptor type- ...) x 2
  • Bone morphogenetic protein 6
KeywordsSIGNALING PROTEIN / TGFB / Signaling / Receptor / Bone Morphogenetic Protein / ALK2 / Ligand / Growth Factor
Function / homology
Function and homology information


positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / Regulation of signaling by NODAL / activin receptor activity / activin receptor activity, type II / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / enzyme activator complex / venous blood vessel development / negative regulation of adherens junction organization ...positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / Regulation of signaling by NODAL / activin receptor activity / activin receptor activity, type II / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / enzyme activator complex / venous blood vessel development / negative regulation of adherens junction organization / endocardial cushion cell fate commitment / positive regulation of chondrocyte differentiation / lymphangiogenesis / trophoblast cell migration / mitral valve morphogenesis / BMP receptor complex / cardiac muscle cell fate commitment / BMP receptor activity / atrial septum primum morphogenesis / endocardial cushion fusion / retina vasculature development in camera-type eye / positive regulation of endothelial cell differentiation / positive regulation of cardiac epithelial to mesenchymal transition / acute inflammatory response / positive regulation of determination of dorsal identity / type B pancreatic cell development / BMP receptor binding / transforming growth factor beta receptor activity, type I / embryonic foregut morphogenesis / smooth muscle cell differentiation / activin receptor complex / activin receptor activity, type I / endocardial cushion formation / artery development / eye development / endochondral ossification / pharyngeal system development / transmembrane receptor protein serine/threonine kinase activity / receptor protein serine/threonine kinase / pattern specification process / activin binding / cellular response to BMP stimulus / male genitalia development / Signaling by BMP / Signaling by Activin / negative regulation of cell-cell adhesion mediated by cadherin / negative regulation of activin receptor signaling pathway / positive regulation of vascular permeability / activin receptor signaling pathway / Signaling by NODAL / embryonic heart tube morphogenesis / gastrulation with mouth forming second / positive regulation of lipopolysaccharide-mediated signaling pathway / dorsal/ventral pattern formation / pancreas development / transforming growth factor beta binding / cartilage development / kinase activator activity / determination of left/right symmetry / negative regulation of ossification / neural crest cell migration / atrioventricular valve morphogenesis / anterior/posterior pattern specification / negative regulation of cold-induced thermogenesis / cell surface receptor protein serine/threonine kinase signaling pathway / insulin secretion / skeletal system morphogenesis / organ growth / growth factor binding / branching involved in blood vessel morphogenesis / ventricular septum morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / SMAD binding / odontogenesis of dentin-containing tooth / mesoderm development / germ cell development / roof of mouth development / peptide hormone binding / positive regulation of intracellular signal transduction / response to magnesium ion / mesoderm formation / positive regulation of SMAD protein signal transduction / regulation of ossification / blood vessel remodeling / BMP signaling pathway / response to retinoic acid / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / response to glucose / negative regulation of signal transduction / positive regulation of endothelial cell proliferation / positive regulation of neuron differentiation / protein serine/threonine/tyrosine kinase activity / transforming growth factor beta receptor signaling pathway / lung development / response to glucocorticoid / protein tyrosine kinase binding / response to activity / cytokine activity / positive regulation of epithelial cell proliferation
Similarity search - Function
GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Transforming growth factor beta, conserved site / Activin types I and II receptor domain / TGF-beta family signature. ...GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Transforming growth factor beta, conserved site / Activin types I and II receptor domain / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Snake toxin-like superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
beta-D-mannopyranose / Bone morphogenetic protein 6 / Activin receptor type-1 / Activin receptor type-2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGoebel, E.J. / Saotome, K. / Franklin, M.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: CryoEM structure of ALK2:BMP6 reveals distinct mechanism that allow ALK2 to interact with both BMP and activin ligands
Authors: Goebel, E.J. / Aykul, S. / Hom, W.W. / Saotome, K. / Economides, A.N. / Franklin, M.C. / Idone, V.J.
History
DepositionFeb 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Activin receptor type-2B
B: Bone morphogenetic protein 6
E: Bone morphogenetic protein 6
F: Activin receptor type-2B
C: Activin receptor type-1
D: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,49916
Polymers87,6386
Non-polymers2,86110
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Activin receptor type- ... , 2 types, 4 molecules AFCD

#1: Protein Activin receptor type-2B / Activin receptor type IIB / ACTR-IIB


Mass: 14933.380 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR2B / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: Q13705, receptor protein serine/threonine kinase
#3: Protein Activin receptor type-1 / Activin receptor type I / ACTR-I / Activin receptor-like kinase 2 / ALK-2 / Serine/threonine- ...Activin receptor type I / ACTR-I / Activin receptor-like kinase 2 / ALK-2 / Serine/threonine-protein kinase receptor R1 / SKR1 / TGF-B superfamily receptor type I / TSR-I


Mass: 13189.880 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR1, ACVRLK2 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: Q04771, receptor protein serine/threonine kinase

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Protein , 1 types, 2 molecules BE

#2: Protein Bone morphogenetic protein 6 / BMP-6 / VG-1-related protein / VG-1-R / VGR-1


Mass: 15695.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP6, VGR / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P22004

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Sugars , 3 types, 10 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of ALK2-ActRIIB with BMP6 / Type: COMPLEX / Details: ALK2-ActRIIB fused by Antibody Hinge region / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.08 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 7.5 / Details: 50mM Tris-HCL, 100mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisC4H11NO31
2100 mMsodium chlorideNaCl1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was mono disperse following purification over size exclusion chromatography.
Specimen supportGrid material: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42185 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: Initial fitting was performed in ChimeraX and real-space refinement was carried out within Phenix.
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeChain-IDInitial refinement model-ID
17YRU

7yru

A7YRUA1
26MAC

6mac

C6MACC2
36OMO

6omo

I6OMOI3

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