+Open data
-Basic information
Entry | Database: PDB / ID: 5hlz | ||||||
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Title | Structure of Pro-Activin A Complex at 2.85 A resolution | ||||||
Components | (Inhibin beta A chain) x 2 | ||||||
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 / negative regulation of G1/S transition of mitotic cell cycle / response to aldosterone / roof of mouth development / eyelid development in camera-type eye / endodermal cell differentiation / 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 / 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 / hormone activity / negative regulation of cell growth / defense response / cytokine-mediated signaling pathway / autophagy / 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 / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / 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: 2.851 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 | 5hlz.cif.gz | 240.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hlz.ent.gz | 192.7 KB | Display | PDB format |
PDBx/mmJSON format | 5hlz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hlz_validation.pdf.gz | 508.8 KB | Display | wwPDB validaton report |
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Full document | 5hlz_full_validation.pdf.gz | 523.6 KB | Display | |
Data in XML | 5hlz_validation.xml.gz | 39.4 KB | Display | |
Data in CIF | 5hlz_validation.cif.gz | 54.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/5hlz ftp://data.pdbj.org/pub/pdb/validation_reports/hl/5hlz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30272.439 Da / Num. of mol.: 4 / Fragment: Pro domain, UNP Residues 30-305 Mutation: C35S, C38S, deletion of K259-D282, furin cleavage site (RRRRR) replaced by HRV 3C protease cleavage site (LEVLFQGP),C35S, C38S, deletion of K259-D282, furin cleavage site replaced by HRV 3C ...Mutation: C35S, C38S, deletion of K259-D282, furin cleavage site (RRRRR) replaced by HRV 3C protease cleavage site (LEVLFQGP),C35S, C38S, deletion of K259-D282, furin cleavage site replaced by HRV 3C protease cleavage site (LEVLFQGP),C35S, C38S, deletion of K259-D282, furin cleavage site (RRRRR) replaced by HRV 3C protease cleavage site (LEVLFQGP),C35S, C38S, deletion of K259-D282, furin cleavage site replaced by HRV 3C protease cleavage site (LEVLFQGP) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INHBA / Details (production host): N-terminal His6-tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08476 #2: Protein | Mass: 12991.865 Da / Num. of mol.: 4 / Fragment: Mature domain, UNP Residues 311-426 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INHBA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08476 #3: 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: 1.67 Å3/Da / Density % sol: 26.24 % / Description: Rods |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% w/v polyethylene glycol 3350, 0.2 M calcium chloride; 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: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2014 / Details: Mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→44.54 Å / Num. obs: 26028 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 36 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.114 / Rsym value: 0.141 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.85→3.01 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.948 / Mean I/σ(I) obs: 1.6 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Structure of the uncleaved growth factor Resolution: 2.851→40.9 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 32.41 / Details: NCS restraint was included in the refinement.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.851→40.9 Å
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Refine LS restraints |
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LS refinement shell |
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