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- PDB-6mac: Ternary structure of GDF11 bound to ActRIIB-ECD and Alk5-ECD -

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Basic information

Entry
Database: PDB / ID: 6mac
TitleTernary structure of GDF11 bound to ActRIIB-ECD and Alk5-ECD
Components
  • Activin receptor type-2B
  • Growth/differentiation factor 11
  • TGF-beta receptor type-1
KeywordsSIGNALING PROTEIN / Growth Factor / Receptor / TGFB / Signaling
Function / homology
Function and homology information


spinal cord anterior/posterior patterning / type B pancreatic cell maturation / negative regulation of amacrine cell differentiation / Signaling by BMP / inhibin binding / activin receptor activity / amacrine cell differentiation / activin receptor activity, type II / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway ...spinal cord anterior/posterior patterning / type B pancreatic cell maturation / negative regulation of amacrine cell differentiation / Signaling by BMP / inhibin binding / activin receptor activity / amacrine cell differentiation / activin receptor activity, type II / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / extracellular structure organization / epicardium morphogenesis / vascular endothelial cell proliferation / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / venous blood vessel development / myofibroblast differentiation / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / Signaling by Activin / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / lymphangiogenesis / trophoblast cell migration / angiogenesis involved in coronary vascular morphogenesis / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of mesenchymal stem cell proliferation / ventricular compact myocardium morphogenesis / positive regulation of extracellular matrix assembly / retina vasculature development in camera-type eye / sexual reproduction / positive regulation of tight junction disassembly / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / TGFBR3 regulates TGF-beta signaling / transforming growth factor beta receptor activity, type I / embryonic foregut morphogenesis / positive regulation of vasculature development / neuron fate commitment / activin receptor complex / activin receptor activity, type I / camera-type eye morphogenesis / regulation of epithelial to mesenchymal transition / artery development / type II transforming growth factor beta receptor binding / pharyngeal system development / transmembrane receptor protein serine/threonine kinase activity / receptor protein serine/threonine kinase / pattern specification process / activin binding / TGFBR1 LBD Mutants in Cancer / germ cell migration / filopodium assembly / coronary artery morphogenesis / embryonic cranial skeleton morphogenesis / activin receptor signaling pathway / ventricular trabecula myocardium morphogenesis / metanephros development / response to cholesterol / gastrulation with mouth forming second / pancreas development / I-SMAD binding / transforming growth factor beta binding / collagen fibril organization / negative regulation of chondrocyte differentiation / kinase activator activity / determination of left/right symmetry / negative regulation of ossification / lens development in camera-type eye / endothelial cell activation / anterior/posterior pattern specification / positive regulation of filopodium assembly / artery morphogenesis / negative regulation of cold-induced thermogenesis / ureteric bud development / insulin secretion / skeletal system morphogenesis / adrenal gland development / organ growth / growth factor binding / ventricular septum morphogenesis / SMAD binding / negative regulation of endothelial cell proliferation / odontogenesis of dentin-containing tooth / mesoderm development / roof of mouth development / TGF-beta receptor signaling activates SMADs / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / blastocyst development / regulation of protein ubiquitination / blood vessel remodeling / regulation of signal transduction / bicellular tight junction / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / BMP signaling pathway / cellular response to transforming growth factor beta stimulus / response to glucose
Similarity search - Function
GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Activin types I and II receptor domain / Transforming growth factor-beta-related ...GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Activin types I and II receptor domain / Transforming growth factor-beta-related / Activin types I and II receptor domain / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Snake toxin-like superfamily / Ribbon / 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 / Mainly Beta
Similarity search - Domain/homology
Growth/differentiation factor 11 / TGF-beta receptor type-1 / Activin receptor type-2B
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsGoebel, E.J. / Thompson, T.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structural characterization of an activin class ternary receptor complex reveals a third paradigm for receptor specificity.
Authors: 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. / ...Authors: 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.
History
DepositionAug 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Growth/differentiation factor 11
C: Activin receptor type-2B
K: TGF-beta receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9015
Polymers32,4593
Non-polymers4422
Water32418
1
A: Growth/differentiation factor 11
C: Activin receptor type-2B
K: TGF-beta receptor type-1
hetero molecules

A: Growth/differentiation factor 11
C: Activin receptor type-2B
K: TGF-beta receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,80210
Polymers64,9186
Non-polymers8854
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area9660 Å2
ΔGint-47 kcal/mol
Surface area31080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.624, 116.624, 56.625
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein Growth/differentiation factor 11 / GDF-11 / Bone morphogenetic protein 11 / BMP-11


Mass: 12357.206 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDF11, BMP11 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O95390
#2: Protein Activin receptor type-2B / Activin receptor type IIB / ACTR-IIB


Mass: 11244.370 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Acvr2b, Actriib / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P38445, receptor protein serine/threonine kinase
#3: Protein TGF-beta receptor type-1 / TGFR-1 / Activin A receptor type II-like protein kinase of 53kD / Activin receptor-like kinase 5 / ...TGFR-1 / Activin A receptor type II-like protein kinase of 53kD / Activin receptor-like kinase 5 / ALK5 / Serine/threonine-protein kinase receptor R4 / SKR4 / TGF-beta type I receptor / Transforming growth factor-beta receptor type I / TbetaR-I


Mass: 8857.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR1, ALK5, SKR4 / Production host: Escherichia coli (E. coli)
References: UniProt: P36897, receptor protein serine/threonine kinase
#4: 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.: 2
Source method: isolated from a genetically manipulated source
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: .05-.15M sodium acetate 12-24% polyethylene glycol 8000 .05-.15M sodium thiocyanate
PH range: 4.5-6.3

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033202 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033202 Å / Relative weight: 1
ReflectionResolution: 2.34→50.5 Å / Num. obs: 18669 / % possible obs: 99.91 % / Redundancy: 2 % / Biso Wilson estimate: 66.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0269 / Rpim(I) all: 0.0269 / Rrim(I) all: 0.038 / Net I/σ(I): 12.07
Reflection shellResolution: 2.34→2.424 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4022 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 1861 / CC1/2: 0.455 / Rpim(I) all: 0.4022 / Rrim(I) all: 0.5687 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E4G, 3KFD, 1NYS

5e4g

3kfd

1nys


Resolution: 2.34→50.5 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 32.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2672 1865 10 %
Rwork0.2217 16791 -
obs0.2261 18656 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.65 Å2 / Biso mean: 73.7106 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.34→50.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2252 0 28 18 2298
Biso mean--76.3 62.87 -
Num. residues----283
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.34-2.40330.37781440.391712881432
2.4033-2.4740.43671440.369212811425
2.474-2.55390.41331440.347312891433
2.5539-2.64520.33711420.30212651407
2.6452-2.75110.31531420.280512871429
2.7511-2.87620.32511390.274412781417
2.8762-3.02790.33151470.265212861433
3.0279-3.21750.31121450.249812971442
3.2175-3.46590.26581390.244512741413
3.4659-3.81460.26091400.225713171457
3.8146-4.36630.23531480.194412921440
4.3663-5.50.20611460.175812901436
5.5-50.51140.27261450.198413471492

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