+Open data
-Basic information
Entry | Database: PDB / ID: 4kxz | ||||||
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Title | crystal structure of tgfb2 in complex with GC2008. | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Cysteine knot / Fab / Various growth functions (TGF-beta) / TGF-beta antagonist (GC2008) / TGF-beta receptors | ||||||
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 / type III transforming growth factor beta receptor binding / pharyngeal arch artery morphogenesis / regulation of transforming growth factor beta2 production / atrial septum morphogenesis / negative regulation of macrophage cytokine production / positive regulation of heart contraction / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / signaling / secondary palate development / positive regulation of stress-activated MAPK cascade / glial cell migration / somatic stem cell division / heart valve morphogenesis / atrial septum primum morphogenesis / endocardial cushion fusion / membranous septum morphogenesis / positive regulation of integrin biosynthetic process / cardiac epithelial to mesenchymal transition / eye development / neural retina development / cranial skeletal system development / embryonic digestive tract development / transforming growth factor beta receptor binding / type II transforming growth factor beta receptor binding / pulmonary valve morphogenesis / cell-cell junction organization / outflow tract septum morphogenesis / negative regulation of Ras protein signal transduction / ventricular trabecula myocardium morphogenesis / collagen fibril organization / embryonic limb morphogenesis / positive regulation of cell adhesion mediated by integrin / dopamine biosynthetic process / embryo development ending in birth or egg hatching / 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 / inner ear development / uterus development / positive regulation of SMAD protein signal transduction / positive regulation of cell division / hemopoiesis / hair follicle development / ECM proteoglycans / neuron development / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / salivary gland morphogenesis / positive regulation of cell cycle / 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 / response to progesterone / kidney development / skeletal system development / cytokine activity / neural tube closure / positive regulation of protein secretion / growth factor activity / wound healing / cell morphogenesis / negative regulation of cell growth / response to wounding / positive regulation of miRNA transcription / male gonad development / positive regulation of neuron apoptotic process / positive regulation of immune response / negative regulation of epithelial cell proliferation / cell migration / Platelet degranulation / amyloid-beta binding / regulation of cell population proliferation / heart development / positive regulation of cell growth / collagen-containing extracellular matrix / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å | ||||||
Authors | Mathieu, M. / Moulin, A.G. / Wei, R. | ||||||
Citation | Journal: Protein Sci. / Year: 2014 Title: Structures of a pan-specific antagonist antibody complexed to different isoforms of TGF beta reveal structural plasticity of antibody-antigen interactions. Authors: Moulin, A. / Mathieu, M. / Lawrence, C. / Bigelow, R. / Levine, M. / Hamel, C. / Marquette, J.P. / Le Parc, J. / Loux, C. / Ferrari, P. / Capdevila, C. / Dumas, J. / Dumas, B. / Rak, A. / ...Authors: Moulin, A. / Mathieu, M. / Lawrence, C. / Bigelow, R. / Levine, M. / Hamel, C. / Marquette, J.P. / Le Parc, J. / Loux, C. / Ferrari, P. / Capdevila, C. / Dumas, J. / Dumas, B. / Rak, A. / Bird, J. / Qiu, H. / Pan, C.Q. / Edmunds, T. / Wei, R.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kxz.cif.gz | 415.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kxz.ent.gz | 352.5 KB | Display | PDB format |
PDBx/mmJSON format | 4kxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/4kxz ftp://data.pdbj.org/pub/pdb/validation_reports/kx/4kxz | HTTPS FTP |
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-Related 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
-Protein , 1 types, 4 molecules ABDE
#1: Protein | Mass: 12732.597 Da / Num. of mol.: 4 / Fragment: unp residues 303-414 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P61812 |
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-Antibody , 2 types, 8 molecules HJNQILMP
#2: Antibody | Mass: 23907.832 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #3: Antibody | Mass: 23425.934 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) |
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-Non-polymers , 3 types, 232 molecules
#4: Chemical | ChemComp-MES / #5: Chemical | ChemComp-PE5 / | #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: 3.17 Å3/Da / Density % sol: 61.24 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 6 Details: 35% PEG400, 100mM MES, VAPOR DIFFUSION, temperature 296K, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.83→48.73 Å / Num. all: 74556 / Num. obs: 74205 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 68.63 Å2 / Rmerge(I) obs: 0.121 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→48.73 Å / Cor.coef. Fo:Fc: 0.9354 / Cor.coef. Fo:Fc free: 0.9069 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.841 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso max: 149.82 Å2 / Biso mean: 51.0971 Å2 / Biso min: 16.86 Å2
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Refine analyze | Luzzati coordinate error obs: 0.334 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.83→48.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.83→2.9 Å / Total num. of bins used: 20
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