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Yorodumi- PDB-7oly: Structure of activin A in complex with an ActRIIB-Alk4 fusion rev... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oly | ||||||
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Title | Structure of activin A in complex with an ActRIIB-Alk4 fusion reveal insight into activin receptor interactions | ||||||
Components |
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Keywords | SIGNALING PROTEIN / GROWTH FACTOR / RECEPTOR / TGFB / SIGNALING | ||||||
Function / homology | Function and homology information Regulation of signaling by NODAL / activin A complex / inhibin A complex / cardiac fibroblast cell development / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / inhibin binding / positive regulation of ovulation / GABAergic neuron differentiation / activin receptor activity, type II ...Regulation of signaling by NODAL / activin A complex / inhibin A complex / cardiac fibroblast cell development / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / inhibin binding / positive regulation of ovulation / GABAergic neuron differentiation / activin receptor activity, type II / 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 / nodal signaling pathway / activin receptor activity / Glycoprotein hormones / negative regulation of macrophage differentiation / venous blood vessel development / positive regulation of follicle-stimulating hormone secretion / cellular response to oxygen-glucose deprivation / hemoglobin biosynthetic process / lymphangiogenesis / retina vasculature development in camera-type eye / positive regulation of trophoblast cell migration / activin receptor activity, type I / embryonic foregut morphogenesis / activin receptor complex / cellular response to follicle-stimulating hormone stimulus / cellular response to cholesterol / artery development / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / Signaling by BMP / activin binding / activin receptor signaling pathway / negative regulation of phosphorylation / Signaling by Activin / SMAD protein signal transduction / Signaling by NODAL / mesodermal cell differentiation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / kinase activator activity / gastrulation with mouth forming second / cellular response to angiotensin / pancreas development / determination of left/right symmetry / skeletal system morphogenesis / negative regulation of cold-induced thermogenesis / insulin secretion / odontogenesis / positive regulation of transcription by RNA polymerase III / anterior/posterior pattern specification / cell surface receptor protein serine/threonine kinase signaling pathway / organ growth / response to aldosterone / negative regulation of G1/S transition of mitotic cell cycle / roof of mouth development / endodermal cell differentiation / eyelid development in camera-type eye / SMAD binding / growth factor binding / odontogenesis of dentin-containing tooth / peptide hormone binding / mesoderm development / positive regulation of SMAD protein signal transduction / negative regulation of type II interferon production / hair follicle development / positive regulation of collagen biosynthetic process / blood vessel remodeling / positive regulation of bone mineralization / BMP signaling pathway / hematopoietic progenitor cell differentiation / positive regulation of osteoblast differentiation / response to glucose / extrinsic apoptotic signaling pathway / ovarian follicle development / positive regulation of protein metabolic process / protein serine/threonine/tyrosine kinase activity / erythrocyte differentiation / post-embryonic development / positive regulation of erythrocyte differentiation / kidney development / cytokine activity / peptidyl-threonine phosphorylation / growth factor activity / lung development / hormone activity / negative regulation of cell growth / cellular response to growth factor stimulus / defense response / autophagy / cytokine-mediated signaling pathway / G1/S transition of mitotic cell cycle / male gonad development / cell-cell signaling / nervous system development Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.265 Å | ||||||
Authors | Hakansson, M. / Rose, N.C. / Castonguay, R. / Logan, D.T. / Krishnan, L. | ||||||
Citation | Journal: Iscience / Year: 2022 Title: Structures of activin ligand traps using natural sets of type I and type II TGF beta receptors. Authors: Goebel, E.J. / Kattamuri, C. / Gipson, G.R. / Krishnan, L. / Chavez, M. / Czepnik, M. / Maguire, M.C. / Grenha, R. / Hakansson, M. / Logan, D.T. / Grinberg, A.V. / Sako, D. / Castonguay, R. ...Authors: Goebel, E.J. / Kattamuri, C. / Gipson, G.R. / Krishnan, L. / Chavez, M. / Czepnik, M. / Maguire, M.C. / Grenha, R. / Hakansson, M. / Logan, D.T. / Grinberg, A.V. / Sako, D. / Castonguay, R. / Kumar, R. / Thompson, T.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oly.cif.gz | 300.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oly.ent.gz | 246.2 KB | Display | PDB format |
PDBx/mmJSON format | 7oly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oly_validation.pdf.gz | 880.4 KB | Display | wwPDB validaton report |
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Full document | 7oly_full_validation.pdf.gz | 888 KB | Display | |
Data in XML | 7oly_validation.xml.gz | 27 KB | Display | |
Data in CIF | 7oly_validation.cif.gz | 36.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/7oly ftp://data.pdbj.org/pub/pdb/validation_reports/ol/7oly | HTTPS FTP |
-Related structure data
Related structure data | 7mrzC 2arvS 5k59S 5macS S: Starting model for refinement C: citing same article (ref.) |
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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
-Activin receptor type- ... , 2 types, 2 molecules CK
#2: Protein | Mass: 14933.380 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR2B / Cell line (production host): CHO / Production host: Homo sapiens (human) References: UniProt: Q13705, receptor protein serine/threonine kinase |
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#4: Protein | Mass: 13122.994 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR1B, ACVRLK4, ALK4 / Cell line (production host): CHO / Production host: Homo sapiens (human) References: UniProt: P36896, receptor protein serine/threonine kinase |
-Antibody , 2 types, 2 molecules HL
#3: Antibody | Mass: 23772.553 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Homo sapiens (human) |
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#5: Antibody | Mass: 24203.885 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Homo sapiens (human) |
-Protein / Non-polymers , 2 types, 16 molecules A
#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 / Cell line (production host): CHO / Production host: Homo sapiens (human) / References: UniProt: P08476 |
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#8: Water | ChemComp-HOH / |
-Sugars , 2 types, 2 molecules
#6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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#7: Sugar | ChemComp-NAG / |
-Details
Has ligand of interest | N |
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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: 3.7 Å3/Da / Density % sol: 66.73 % / Description: Disc-shaped |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 17.7 mg/ml complex in 20 mM HEPES, 200 mM NaCl pH 7.5. 100 + 100 nl sitting drop in a MRC 3-well plate with reservoir 0.1 M Na cacodylate pH 6.5 and 17 % (w/v) PEG 4000). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.992 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.992 Å / Relative weight: 1 |
Reflection | Resolution: 3.26→49.25 Å / Num. obs: 23230 / % possible obs: 99.9 % / Redundancy: 35.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.317 / Rpim(I) all: 0.054 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 3.26→3.39 Å / Rmerge(I) obs: 2.667 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4489 / CC1/2: 0.504 / Rpim(I) all: 0.446 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5K59, 5MAC, 2ARV Resolution: 3.265→49.25 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 5.022 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.449 / SU Rfree Cruickshank DPI: 0.436
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Displacement parameters | Biso mean: 112.97 Å2
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Refine analyze | Luzzati coordinate error obs: 0.48 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.265→49.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.27→3.29 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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