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- PDB-1nyu: Crystal Structure of Activin A Bound to the ECD of ActRIIB -

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Basic information

Entry
Database: PDB / ID: 1nyu
TitleCrystal Structure of Activin A Bound to the ECD of ActRIIB
Components
  • Inhibin beta A chain
  • activin receptor
KeywordsMEMBRANE PROTEIN/HORMONE/GROWTH FACTOR / ACTIVIN / TYPE II / TGF BETA / ACTRIIB / EXTRACELLULAR DOMAIN / MEMBRANE PROTEIN-HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


Signaling by BMP / inhibin binding / activin A complex / inhibin A complex / cardiac fibroblast cell development / transforming growth factor beta receptor activity, type III / androst-4-ene-3,17-dione biosynthetic process / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / positive regulation of ovulation ...Signaling by BMP / inhibin binding / activin A complex / inhibin A complex / cardiac fibroblast cell development / transforming growth factor beta receptor activity, type III / androst-4-ene-3,17-dione biosynthetic process / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / positive regulation of ovulation / activin receptor activity / negative regulation of follicle-stimulating hormone secretion / GABAergic neuron differentiation / Antagonism of Activin by Follistatin / TGFBR3 regulates activin signaling / type II activin receptor binding / activin receptor activity, type II / progesterone secretion / lymphatic endothelial cell differentiation / Sertoli cell differentiation / striatal medium spiny neuron differentiation / positive regulation of activin receptor signaling pathway / transforming growth factor beta receptor activity, type II / enzyme activator complex / Glycoprotein hormones / negative regulation of macrophage differentiation / negative regulation of phosphorylation / positive regulation of follicle-stimulating hormone secretion / cellular response to oxygen-glucose deprivation / venous blood vessel development / hemoglobin biosynthetic process / Signaling by Activin / lymphangiogenesis / testosterone biosynthetic process / BMP receptor activity / retina vasculature development in camera-type eye / sexual reproduction / embryonic foregut morphogenesis / transforming growth factor beta receptor activity, type I / activin receptor complex / cellular response to follicle-stimulating hormone stimulus / activin receptor activity, type I / artery development / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / cellular response to cholesterol / pattern specification process / activin binding / SMAD protein signal transduction / Signaling by BMP / Signaling by Activin / activin receptor signaling pathway / response to aldosterone / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / gastrulation with mouth forming second / mesodermal cell differentiation / pancreas development / kinase activator activity / determination of left/right symmetry / insulin secretion / odontogenesis / anterior/posterior pattern specification / negative regulation of cold-induced thermogenesis / skeletal system morphogenesis / positive regulation of transcription by RNA polymerase III / adrenal gland development / organ growth / negative regulation of G1/S transition of mitotic cell cycle / growth factor binding / endodermal cell differentiation / eyelid development in camera-type eye / odontogenesis of dentin-containing tooth / positive regulation of protein metabolic process / mesoderm development / peptide hormone binding / roof of mouth development / negative regulation of type II interferon production / androgen metabolic process / cellular response to angiotensin / blood vessel remodeling / positive regulation of SMAD protein signal transduction / positive regulation of collagen biosynthetic process / hair follicle development / regulation of signal transduction / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / response to glucose / hematopoietic progenitor cell differentiation / ovarian follicle development / extrinsic apoptotic signaling pathway / protein serine/threonine/tyrosine kinase activity / positive regulation of erythrocyte differentiation / erythrocyte differentiation / response to activity / cytokine activity / skeletal system development / post-embryonic development / growth factor activity / kidney development
Similarity search - Function
Inhibin, beta A subunit / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal ...Inhibin, beta A subunit / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor beta, conserved site / 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. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / 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 / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Inhibin beta A chain / Activin receptor type-2B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsThompson, T.B. / Woodruff, T.K. / Jardetzky, T.S.
CitationJournal: EMBO J. / Year: 2003
Title: Structures of an ActRIIB:activin A complex reveal a novel binding mode for TGF-beta ligand:receptor interactions
Authors: Thompson, T.B. / Woodruff, T.K. / Jardetzky, T.S.
History
DepositionFeb 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 30, 2012Group: Database references
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: activin receptor
B: Inhibin beta A chain
C: activin receptor
D: Inhibin beta A chain


Theoretical massNumber of molelcules
Total (without water)50,6674
Polymers50,6674
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.330, 141.330, 46.021
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein activin receptor


Mass: 12341.596 Da / Num. of mol.: 2 / Fragment: N-terminal Extracellular Domain (residues 19-119)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: actrIIb / Plasmid: pvl1392 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF+ / References: UniProt: P38445
#2: Protein Inhibin beta A chain / Activin beta-A chain / Erythroid differentiation protein / EDF


Mass: 12991.865 Da / Num. of mol.: 2 / Fragment: Mature Domain (residues 311-426)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INHBA / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): BA83.6-02 / References: UniProt: P08476
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: 3.45 Å3/Da / Density % sol: 64.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, sodium chloride, hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17-10 mg/mlprotein1drop
220 mMHEPES1drop
3150 mM1droppH7.5NaCl
427 %PEG40001reservoir
5250 mM1reservoirNaCl
6100 mMHEPES1reservoirpH7.0

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 28, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→14.99 Å / Num. obs: 8777 / % possible obs: 99.5 % / Redundancy: 14.5 % / Biso Wilson estimate: 95.8 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 31.1
Reflection shellResolution: 3.1→3.15 Å / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 5.9
Reflection
*PLUS
Lowest resolution: 15 Å / Num. obs: 8815 / % possible obs: 97.6 % / Num. measured all: 128261
Reflection shell
*PLUS
% possible obs: 95.6 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
BRUTEphasing
BEASTphasing
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BTE

1bte


Resolution: 3.1→14.99 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.291 657 7.5 %RANDOM
Rwork0.268 ---
all0.269 ---
obs0.268 8777 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.2202 Å2 / ksol: 0.262393 e/Å3
Displacement parametersBiso mean: 95.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.06 Å20 Å20 Å2
2--3.06 Å20 Å2
3----6.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 3.1→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 0 0 2375
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d28
X-RAY DIFFRACTIONc_improper_angle_d1.02
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 107 7.5 %
Rwork0.312 1329 -
obs-1436 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0096
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg28
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02
LS refinement shell
*PLUS
Lowest resolution: 3.15 Å

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