+Open data
-Basic information
Entry | Database: PDB / ID: 4kv5 | |||||||||
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Title | scFv GC1009 in complex with TGF-beta1. | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Cysteine knot / Fab / TGF-beta receptor mimetic / TGF-beta / TGF-beta receptor | |||||||||
Function / homology | Function and homology information positive regulation of primary miRNA processing / positive regulation of microglia differentiation / Influenza Virus Induced Apoptosis / negative regulation of skeletal muscle tissue development / TGFBR2 MSI Frameshift Mutants in Cancer / regulatory T cell differentiation / regulation of blood vessel remodeling / regulation of striated muscle tissue development / extracellular matrix assembly / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target ...positive regulation of primary miRNA processing / positive regulation of microglia differentiation / Influenza Virus Induced Apoptosis / negative regulation of skeletal muscle tissue development / TGFBR2 MSI Frameshift Mutants in Cancer / regulatory T cell differentiation / regulation of blood vessel remodeling / regulation of striated muscle tissue development / extracellular matrix assembly / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / regulation of protein import into nucleus / embryonic liver development / type III transforming growth factor beta receptor binding / negative regulation of hyaluronan biosynthetic process / positive regulation of cardiac muscle cell differentiation / myofibroblast differentiation / odontoblast differentiation / connective tissue replacement involved in inflammatory response wound healing / positive regulation of receptor signaling pathway via STAT / negative regulation of macrophage cytokine production / TGFBR2 Kinase Domain Mutants in Cancer / positive regulation of isotype switching to IgA isotypes / positive regulation of mesenchymal stem cell proliferation / membrane protein intracellular domain proteolysis / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / heart valve morphogenesis / positive regulation of vasculature development / hyaluronan catabolic process / regulation of transforming growth factor beta receptor signaling pathway / ATP biosynthetic process / receptor catabolic process / positive regulation of extracellular matrix assembly / negative regulation of extracellular matrix disassembly / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / positive regulation of chemotaxis / type I transforming growth factor beta receptor binding / negative regulation of biomineral tissue development / cell-cell junction organization / negative regulation of myoblast differentiation / positive regulation of vascular permeability / deubiquitinase activator activity / positive regulation of endothelial cell apoptotic process / response to cholesterol / positive regulation of chemokine (C-X-C motif) ligand 2 production / aortic valve morphogenesis / positive regulation of fibroblast migration / phosphate-containing compound metabolic process / negative regulation of protein localization to plasma membrane / sprouting angiogenesis / neural tube development / Molecules associated with elastic fibres / RUNX3 regulates CDKN1A transcription / positive regulation of epidermal growth factor receptor signaling pathway / ventricular cardiac muscle tissue morphogenesis / negative regulation of fat cell differentiation / macrophage derived foam cell differentiation / Syndecan interactions / negative regulation of cell-cell adhesion / positive regulation of interleukin-17 production / negative regulation of blood vessel endothelial cell migration / TGF-beta receptor signaling activates SMADs / negative regulation of cell differentiation / positive regulation of SMAD protein signal transduction / RUNX3 regulates p14-ARF / positive regulation of cell division / cellular response to low-density lipoprotein particle stimulus / negative regulation of cell cycle / ECM proteoglycans / positive regulation of vascular endothelial growth factor production / epithelial to mesenchymal transition / positive regulation of collagen biosynthetic process / positive regulation of epithelial to mesenchymal transition / positive regulation of blood vessel endothelial cell migration / lymph node development / vasculogenesis / chondrocyte differentiation / hematopoietic progenitor cell differentiation / salivary gland morphogenesis / regulation of cell migration / extrinsic apoptotic signaling pathway / positive regulation of protein dephosphorylation / cellular response to transforming growth factor beta stimulus / antigen binding / extracellular matrix / positive regulation of protein metabolic process / protein export from nucleus / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / positive regulation of superoxide anion generation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / negative regulation of miRNA transcription / negative regulation of protein phosphorylation / platelet alpha granule lumen / response to progesterone / cytokine activity / neural tube closure / positive regulation of protein secretion / positive regulation of protein-containing complex assembly Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å | |||||||||
Authors | Wei, R. / Moulin, A.G. / Mathieu, M. | |||||||||
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 | 4kv5.cif.gz | 262.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kv5.ent.gz | 221.4 KB | Display | PDB format |
PDBx/mmJSON format | 4kv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/4kv5 ftp://data.pdbj.org/pub/pdb/validation_reports/kv/4kv5 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 12809.812 Da / Num. of mol.: 4 / Fragment: unp residues 279-390 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB1, TGFB / Production host: Escherichia coli (E. coli) / References: UniProt: P01137 #2: Antibody | Mass: 26656.588 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2 (DE3) |
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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: 3.01 Å3/Da / Density % sol: 59.15 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 5 Details: 16% PEG 4K, 0.1 M citrate, 4% 2-propanol , pH 5.0, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: May 15, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→30.96 Å / Num. all: 36102 / Num. obs: 36020 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30.96 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.5 / σ(F): 0 / Phase error: 34.45 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.0874 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→30.96 Å
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Refine LS restraints |
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LS refinement shell |
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