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Yorodumi- PDB-6xm2: The structure of the 4A11.v7 antibody in complex with human TGFb2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xm2 | ||||||
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Title | The structure of the 4A11.v7 antibody in complex with human TGFb2 | ||||||
Components |
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Keywords | CYTOKINE/IMMUNE SYSTEM / TGFb antibody / CYTOKINE / CYTOKINE-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / substantia propria of cornea development / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / ascending aorta morphogenesis / uterine wall breakdown / cardioblast differentiation / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / cardiac right ventricle morphogenesis ...regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / substantia propria of cornea development / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / ascending aorta morphogenesis / uterine wall breakdown / cardioblast differentiation / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / cardiac right ventricle morphogenesis / pharyngeal arch artery morphogenesis / type III transforming growth factor beta receptor binding / regulation of transforming growth factor beta2 production / atrial septum morphogenesis / positive regulation of heart contraction / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / negative regulation of macrophage cytokine production / signaling / secondary palate development / glial cell migration / positive regulation of stress-activated MAPK cascade / somatic stem cell division / heart valve morphogenesis / endocardial cushion fusion / atrial septum primum morphogenesis / membranous septum morphogenesis / positive regulation of integrin biosynthetic process / cardiac epithelial to mesenchymal transition / eye development / cranial skeletal system development / neural retina development / embryonic digestive tract development / transforming growth factor beta receptor binding / type II transforming growth factor beta receptor binding / pulmonary valve morphogenesis / outflow tract septum morphogenesis / ventricular trabecula myocardium morphogenesis / cell-cell junction organization / negative regulation of Ras protein signal transduction / collagen fibril organization / positive regulation of cell adhesion mediated by integrin / embryonic limb morphogenesis / embryo development ending in birth or egg hatching / dopamine biosynthetic process / odontogenesis / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / cardiac muscle cell proliferation / endocardial cushion morphogenesis / generation of neurons / hair follicle morphogenesis / ventricular septum morphogenesis / positive regulation of epithelial cell migration / positive regulation of Notch signaling pathway / activation of protein kinase activity / TGF-beta receptor signaling activates SMADs / uterus development / positive regulation of SMAD protein signal transduction / inner ear development / hemopoiesis / positive regulation of cell division / hair follicle development / ECM proteoglycans / neuron development / epithelial to mesenchymal transition / positive regulation of cell cycle / salivary gland morphogenesis / positive regulation of epithelial to mesenchymal transition / heart morphogenesis / extrinsic apoptotic signaling pathway / epithelial cell differentiation / negative regulation of angiogenesis / neutrophil chemotaxis / transforming growth factor beta receptor signaling pathway / platelet alpha granule lumen / skeletal system development / kidney development / response to progesterone / cytokine activity / neural tube closure / positive regulation of protein secretion / growth factor activity / wound healing / cell morphogenesis / negative regulation of cell growth / positive regulation of miRNA transcription / response to wounding / negative regulation of epithelial cell proliferation / male gonad development / positive regulation of immune response / positive regulation of neuron apoptotic process / cell migration / Platelet degranulation / heart development / amyloid-beta binding / regulation of cell population proliferation / positive regulation of cell growth / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to hypoxia Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.91 Å | ||||||
Authors | Lupardus, P.J. / Yin, J.P. | ||||||
Citation | Journal: Sci Transl Med / Year: 2021 Title: TGF beta 2 and TGF beta 3 isoforms drive fibrotic disease pathogenesis. Authors: Sun, T. / Huang, Z. / Liang, W.C. / Yin, J. / Lin, W.Y. / Wu, J. / Vernes, J.M. / Lutman, J. / Caplazi, P. / Jeet, S. / Wong, T. / Wong, M. / DePianto, D.J. / Morshead, K.B. / Sun, K.H. / ...Authors: Sun, T. / Huang, Z. / Liang, W.C. / Yin, J. / Lin, W.Y. / Wu, J. / Vernes, J.M. / Lutman, J. / Caplazi, P. / Jeet, S. / Wong, T. / Wong, M. / DePianto, D.J. / Morshead, K.B. / Sun, K.H. / Modrusan, Z. / Vander Heiden, J.A. / Abbas, A.R. / Zhang, H. / Xu, M. / N'Diaye, E.N. / Roose-Girma, M. / Wolters, P.J. / Yadav, R. / Sukumaran, S. / Ghilardi, N. / Corpuz, R. / Emson, C. / Meng, Y.G. / Ramalingam, T.R. / Lupardus, P. / Brightbill, H.D. / Seshasayee, D. / Wu, Y. / Arron, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xm2.cif.gz | 426.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xm2.ent.gz | 347.1 KB | Display | PDB format |
PDBx/mmJSON format | 6xm2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/6xm2 ftp://data.pdbj.org/pub/pdb/validation_reports/xm/6xm2 | HTTPS FTP |
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-Related structure data
Related structure data | 4kxzS 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23673.074 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #2: Antibody | Mass: 24372.275 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Protein | Mass: 12732.597 Da / Num. of mol.: 4 / Fragment: mature domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P61812 #4: 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: 2.44 Å3/Da / Density % sol: 49.68 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 1000, 0.1 M Tris pH8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→82.97 Å / Num. obs: 161613 / % possible obs: 90.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 31.75 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.91→2.01 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8036 / CC1/2: 0.877 / % possible all: 88.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KXZ Resolution: 1.91→82.97 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 123.06 Å2 / Biso mean: 41.6117 Å2 / Biso min: 17.9 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→82.97 Å
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