+Open data
-Basic information
Entry | Database: PDB / ID: 1nyu | ||||||
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Title | Crystal Structure of Activin A Bound to the ECD of ActRIIB | ||||||
Components |
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Keywords | MEMBRANE 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 / 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 ...Signaling by BMP / 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 / 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 / hemoglobin biosynthetic process / retina vasculature development in camera-type eye / sexual reproduction / 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 / 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 / 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 / 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 / skeletal system development / cytokine activity / lung development / growth factor activity / defense response / hormone activity / negative regulation of cell growth / cellular response to growth factor stimulus / autophagy / cytokine-mediated signaling pathway / male gonad development / cell-cell signaling / nervous system development / heart development / cellular response to hypoxia Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Thompson, T.B. / Woodruff, T.K. / Jardetzky, T.S. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nyu.cif.gz | 69.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nyu.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 1nyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/1nyu ftp://data.pdbj.org/pub/pdb/validation_reports/ny/1nyu | HTTPS FTP |
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-Related structure data
Related structure data | 1nysC 1bteS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | 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
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.11 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 28, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BTE Resolution: 3.1→14.99 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.2202 Å2 / ksol: 0.262393 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 95.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→14.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 3.15 Å |