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- PDB-1nys: Crystal Structure of Activin A Bound to the ECD of ActRIIB P41 -

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Basic information

Entry
Database: PDB / ID: 1nys
TitleCrystal Structure of Activin A Bound to the ECD of ActRIIB P41
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-betaglycan-ActRII complex / activin A complex / inhibin A complex / cardiac fibroblast cell development / : / regulation of follicle-stimulating hormone secretion / inhibin binding / negative regulation of B cell differentiation / positive regulation of ovulation ...Signaling by BMP / inhibin-betaglycan-ActRII complex / activin A complex / inhibin A complex / cardiac fibroblast cell development / : / regulation of follicle-stimulating hormone secretion / inhibin binding / negative regulation of B cell differentiation / positive regulation of ovulation / GABAergic neuron differentiation / Antagonism of Activin by Follistatin / negative regulation of follicle-stimulating hormone secretion / progesterone secretion / penile erection / lymphatic endothelial cell differentiation / type II activin receptor binding / striatal medium spiny neuron differentiation / positive regulation of activin receptor signaling pathway / activin receptor activity / negative regulation of macrophage differentiation / Glycoprotein hormones / lymphangiogenesis / venous blood vessel development / positive regulation of follicle-stimulating hormone secretion / cellular response to oxygen-glucose deprivation / Signaling by Activin / Sertoli cell proliferation / sperm ejaculation / hemoglobin biosynthetic process / retina vasculature development in camera-type eye / sexual reproduction / BMP receptor activity / embryonic skeletal system development / embryonic foregut morphogenesis / activin receptor complex / cellular response to follicle-stimulating hormone stimulus / cellular response to cholesterol / pattern specification process / artery development / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / Signaling by BMP / activin binding / negative regulation of phosphorylation / cellular response to BMP stimulus / activin receptor signaling pathway / Signaling by Activin / kinase activator activity / mesodermal cell differentiation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / SMAD protein signal transduction / gastrulation with mouth forming second / pancreas development / cellular response to angiotensin / determination of left/right symmetry / skeletal system morphogenesis / positive regulation of transcription by RNA polymerase III / negative regulation of cold-induced thermogenesis / insulin secretion / odontogenesis / anterior/posterior pattern specification / organ growth / regulation of nitric-oxide synthase activity / adrenal gland development / response to aldosterone / negative regulation of G1/S transition of mitotic cell cycle / roof of mouth development / eyelid development in camera-type eye / endodermal cell differentiation / odontogenesis of dentin-containing tooth / growth factor binding / mesoderm development / peptide hormone binding / positive regulation of SMAD protein signal transduction / negative regulation of type II interferon production / hair follicle development / positive regulation of collagen biosynthetic process / regulation of signal transduction / blood vessel remodeling / positive regulation of osteoblast differentiation / BMP signaling pathway / hematopoietic progenitor cell differentiation / positive regulation of bone mineralization / response to glucose / coreceptor activity / extrinsic apoptotic signaling pathway / ovarian follicle development / positive regulation of protein metabolic process / protein serine/threonine/tyrosine kinase activity / post-embryonic development / erythrocyte differentiation / response to activity / positive regulation of erythrocyte differentiation / kidney development / response to organic substance / skeletal system development / cytokine activity / PDZ domain binding / lung development
Similarity search - Function
Inhibin, beta A subunit / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor-beta, C-terminal ...Inhibin, beta A subunit / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Activin types I and II receptor domain / Activin types I and II receptor domain / 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 / Snake toxin-like superfamily / Cystine-knot cytokine / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Inhibin beta A chain / Activin receptor type-2A / Activin receptor type-2B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 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 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 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
Remark 999SEQUENCE According to the depositor, Pro64 is a DNA sequence error in the database (PIR JQ1484). ...SEQUENCE According to the depositor, Pro64 is a DNA sequence error in the database (PIR JQ1484). The correct residue is Arg64. This has been confirmed by sequence alignment of orthologous proteins.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.954, 104.954, 46.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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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: P38444, UniProt: P38445*PLUS
#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

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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: 64.06 %
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: May 11, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→25 Å / Num. obs: 9789 / % possible obs: 93.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 77 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.14
Reflection shellResolution: 3.05→3.1 Å / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.9
Reflection
*PLUS
Num. measured all: 44194
Reflection shell
*PLUS
% possible obs: 87 %

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Processing

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

1bte


Resolution: 3.05→24.74 Å / Rfactor Rfree error: 0.014 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.299 484 5.2 %RANDOM
Rwork0.252 ---
all0.28 ---
obs0.252 9254 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.6845 Å2 / ksol: 0.270069 e/Å3
Displacement parametersBiso mean: 77 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å20 Å20 Å2
2--2.51 Å20 Å2
3----5.03 Å2
Refine analyzeLuzzati coordinate error free: 0.52 Å / Luzzati sigma a free: 0.72 Å
Refinement stepCycle: LAST / Resolution: 3.05→24.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 0 0 2635
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 3.05→3.24 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.435 61 4.3 %
Rwork0.357 1346 -
obs--87.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rfree: 0.298 / Rfactor Rwork: 0.251 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.84
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96
LS refinement shell
*PLUS
Lowest resolution: 3.1 Å

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