+Open data
-Basic information
Entry | Database: PDB / ID: 5hly | ||||||
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Title | Structure of Pro-Activin A Precursor at 2.3 A Resolution | ||||||
Components | Inhibin beta A chain | ||||||
Keywords | SIGNALING PROTEIN / Growth factor / Precursor / Signalling | ||||||
Function / homology | Function and homology information 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 ...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 / Glycoprotein hormones / negative regulation of macrophage differentiation / positive regulation of follicle-stimulating hormone secretion / cellular response to oxygen-glucose deprivation / hemoglobin biosynthetic process / cellular response to follicle-stimulating hormone stimulus / cellular response to cholesterol / Signaling by BMP / activin receptor signaling pathway / negative regulation of phosphorylation / Signaling by Activin / SMAD protein signal transduction / mesodermal cell differentiation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / cellular response to angiotensin / odontogenesis / positive regulation of transcription by RNA polymerase III / 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 / positive regulation of SMAD protein signal transduction / peptide hormone binding / negative regulation of type II interferon production / hair follicle development / 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 / cytokine activity / growth factor activity / negative regulation of cell growth / hormone activity / defense response / autophagy / cytokine-mediated signaling pathway / male gonad development / cell-cell signaling / nervous system development / cellular response to hypoxia / transcription by RNA polymerase II / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / cell differentiation / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / protein-containing complex binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 Å | ||||||
Authors | Wang, X. / Fischer, G. / Hyvonen, M. | ||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Structure and activation of pro-activin A. Authors: Wang, X. / Fischer, G. / Hyvonen, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hly.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hly.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 5hly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/5hly ftp://data.pdbj.org/pub/pdb/validation_reports/hl/5hly | HTTPS FTP |
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-Related 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: 43664.020 Da / Num. of mol.: 1 / Mutation: C35S, C38S, deletion:K259-D282 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INHBA / Plasmid: pUBS520 / Details (production host): N-terminal His6-tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08476 |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Description: rods |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% w/v polyethylene glycol 1000, 100 mM MES pH 6.5; cryo: 15% v/v PEG 400 added |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97866 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2014 / Details: Mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97866 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→74.15 Å / Num. obs: 11247 / % possible obs: 79.3 % / Observed criterion σ(I): -3 / Redundancy: 14.3 % / Biso Wilson estimate: 38.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rsym value: 0.114 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.4 / % possible all: 37.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: experimental phases from separate dataset Resolution: 2.302→74.15 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 2.05 / Phase error: 22.9 / Details: anomalous Se signal used in refinement
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.302→74.15 Å
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Refine LS restraints |
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LS refinement shell |
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