+Open data
-Basic information
Entry | Database: PDB / ID: 2arp | ||||||
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Title | Activin A in complex with Fs12 fragment of follistatin | ||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR / cystine knot / disulfide rich / egf domain / kazal domain / protein complex / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | Function and homology information Antagonism of Activin by Follistatin / activin receptor antagonist activity / activin A complex / inhibin A complex / cardiac fibroblast cell development / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / positive regulation of ovulation / GABAergic neuron differentiation / Antagonism of Activin by Follistatin ...Antagonism of Activin by Follistatin / activin receptor antagonist activity / activin A complex / inhibin A complex / cardiac fibroblast cell development / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / positive regulation of ovulation / GABAergic neuron differentiation / Antagonism of Activin by Follistatin / negative regulation of follicle-stimulating hormone secretion / progesterone secretion / type II activin receptor binding / striatal medium spiny neuron differentiation / ameloblast differentiation / Glycoprotein hormones / negative regulation of macrophage differentiation / cellular response to oxygen-glucose deprivation / positive regulation of follicle-stimulating hormone secretion / hemoglobin biosynthetic process / positive regulation of hair follicle development / regulation of BMP signaling pathway / gamete generation / cellular response to follicle-stimulating hormone stimulus / cellular response to cholesterol / pattern specification process / activin binding / eyelid development in camera-type eye / Signaling by BMP / activin receptor signaling pathway / negative regulation of phosphorylation / SMAD protein signal transduction / negative regulation of activin receptor signaling pathway / Signaling by Activin / mesodermal cell differentiation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / heparan sulfate proteoglycan binding / cellular response to angiotensin / odontogenesis / hair follicle development / positive regulation of transcription by RNA polymerase III / negative regulation of epithelial cell differentiation / hair follicle morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / response to aldosterone / female gonad development / roof of mouth development / BMP signaling pathway / endodermal cell differentiation / odontogenesis of dentin-containing tooth / peptide hormone binding / positive regulation of SMAD protein signal transduction / negative regulation of type II interferon production / keratinocyte proliferation / positive regulation of collagen biosynthetic process / hematopoietic progenitor cell differentiation / extrinsic apoptotic signaling pathway / ovarian follicle development / positive regulation of protein metabolic process / erythrocyte differentiation / positive regulation of erythrocyte differentiation / skeletal system development / cytokine activity / growth factor activity / hormone activity / response to organic cyclic compound / negative regulation of cell growth / cellular response to growth factor stimulus / defense response / cytokine-mediated signaling pathway / autophagy / male gonad development / cell-cell signaling / cellular response to hypoxia / nervous system development / transcription by RNA polymerase II / positive regulation of ERK1 and ERK2 cascade / cell differentiation / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / regulation of transcription by RNA polymerase II / positive regulation of gene expression / positive regulation of DNA-templated transcription / protein-containing complex binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Harrington, A.E. / Morris-Triggs, S.A. / Ruotolo, B.T. / Robinson, C.V. / Ohnuma, S. / Hyvonen, M. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: Structural basis for the inhibition of activin signalling by follistatin Authors: Harrington, A.E. / Morris-Triggs, S.A. / Ruotolo, B.T. / Robinson, C.V. / Ohnuma, S. / Hyvonen, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2arp.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2arp.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 2arp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2arp_validation.pdf.gz | 767.8 KB | Display | wwPDB validaton report |
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Full document | 2arp_full_validation.pdf.gz | 778 KB | Display | |
Data in XML | 2arp_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 2arp_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/2arp ftp://data.pdbj.org/pub/pdb/validation_reports/ar/2arp | HTTPS FTP |
-Related structure data
Related structure data | 2arvC 1lr9S 1s4uS 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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Details | The second part of the biological assembly is generated by the two fold axis: -X,-Y,Z. |
-Components
-Protein , 2 types, 2 molecules AF
#1: Protein | Mass: 12991.865 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INHBA / Plasmid: pBAT4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08476 |
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#2: Protein | Mass: 16593.193 Da / Num. of mol.: 1 / Fragment: Fs1-Fs2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fst / Plasmid: pHAT4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21674 |
-Non-polymers , 4 types, 179 molecules
#3: Chemical | #4: Chemical | ChemComp-1PG / | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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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: 2.9 Å3/Da / Density % sol: 56.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG-MME 2000, Nickel chloride, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97926 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 23, 2005 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2→25.8 Å / Num. obs: 23201 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 32.33 Å2 / Rsym value: 0.055 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.67 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries: 1s4u, 1lr9 Resolution: 2→25.8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.14 / SU ML: 0.108 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.674 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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