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- PDB-6t9e: Crystal structure of a bispecific DutaFab in complex with human PDGF -
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Open data
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Basic information
Entry | Database: PDB / ID: 6t9e | ||||||
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Title | Crystal structure of a bispecific DutaFab in complex with human PDGF | ||||||
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![]() | IMMUNE SYSTEM / monoclonal antibody / bispecific antibody / Fab fragment / PDGF | ||||||
Function / homology | ![]() metanephric glomerular mesangial cell development / positive regulation of vascular associated smooth muscle cell dedifferentiation / platelet-derived growth factor complex / positive regulation of metanephric mesenchymal cell migration / negative regulation of phosphatidylinositol biosynthetic process / positive regulation of glomerular filtration / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / cellular response to mycophenolic acid / negative regulation of vascular associated smooth muscle cell differentiation / superoxide-generating NADPH oxidase activator activity ...metanephric glomerular mesangial cell development / positive regulation of vascular associated smooth muscle cell dedifferentiation / platelet-derived growth factor complex / positive regulation of metanephric mesenchymal cell migration / negative regulation of phosphatidylinositol biosynthetic process / positive regulation of glomerular filtration / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / cellular response to mycophenolic acid / negative regulation of vascular associated smooth muscle cell differentiation / superoxide-generating NADPH oxidase activator activity / protein kinase C signaling / positive regulation of hyaluronan biosynthetic process / platelet-derived growth factor binding / positive regulation of glomerular mesangial cell proliferation / interleukin-18-mediated signaling pathway / positive regulation of chemotaxis / Signaling by PDGF / paracrine signaling / platelet-derived growth factor receptor binding / positive regulation of vascular associated smooth muscle cell migration / positive regulation of cell-substrate adhesion / positive regulation of DNA biosynthetic process / cellular response to platelet-derived growth factor stimulus / positive regulation of smooth muscle cell migration / positive regulation of calcium ion import / chemoattractant activity / monocyte chemotaxis / positive regulation of cell division / platelet-derived growth factor receptor signaling pathway / Non-integrin membrane-ECM interactions / negative regulation of platelet activation / embryonic placenta development / positive regulation of blood vessel endothelial cell migration / positive regulation of protein autophosphorylation / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of endothelial cell proliferation / collagen binding / reactive oxygen species metabolic process / Downstream signal transduction / positive regulation of mitotic nuclear division / cell chemotaxis / negative regulation of miRNA transcription / platelet alpha granule lumen / negative regulation of protein binding / positive regulation of smooth muscle cell proliferation / growth factor activity / positive regulation of MAP kinase activity / cellular response to growth factor stimulus / positive regulation of miRNA transcription / response to wounding / Golgi lumen / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of reactive oxygen species metabolic process / positive regulation of fibroblast proliferation / Platelet degranulation / PIP3 activates AKT signaling / heart development / gene expression / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / basolateral plasma membrane / collagen-containing extracellular matrix / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / positive regulation of cell migration / protein heterodimerization activity / endoplasmic reticulum lumen / Golgi membrane / negative regulation of gene expression / protein phosphorylation / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of gene expression / positive regulation of DNA-templated transcription / cell surface / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kimbung, R. / Logan, D.T. / Beckmann, R. / Jensen, K. / Speck, J. / Fenn, S. / Kettenberger, H. | ||||||
![]() | ![]() Title: DutaFabs are engineered therapeutic Fab fragments that can bind two targets simultaneously. Authors: Beckmann, R. / Jensen, K. / Fenn, S. / Speck, J. / Krause, K. / Meier, A. / Roth, M. / Fauser, S. / Kimbung, R. / Logan, D.T. / Steegmaier, M. / Kettenberger, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 213.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475 KB | Display | ![]() |
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Full document | ![]() | 504.6 KB | Display | |
Data in XML | ![]() | 38.2 KB | Display | |
Data in CIF | ![]() | 51.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6t9dC ![]() 4qciS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
#1: Antibody | Mass: 23502.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 23923.521 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein | Mass: 12313.501 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Human platelet-derived growth factor subunit B purchased from Peprotech Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.5 % / Description: Plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: DutaFab and PDGF-BB (Peprotech, catalogue number 100-13A) were mixed at a 1:1 molar ratio in relation to PDGF monomer. The complex was concentrated to 12 mg/ml and crystallization was ...Details: DutaFab and PDGF-BB (Peprotech, catalogue number 100-13A) were mixed at a 1:1 molar ratio in relation to PDGF monomer. The complex was concentrated to 12 mg/ml and crystallization was performed by hanging drop vapour diffusion against 0.1 M Tris pH 7.5, 42 % 2-methyl-2,4-pentanediol (MPD) at 20 C. Plate-shaped crystals grew within a few weeks and were frozen in liquid nitrogen with 20% glycerol as cryo-protectant. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 3, 2015 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.989→30 Å / Num. obs: 29016 / % possible obs: 97.7 % / Redundancy: 3 % / Biso Wilson estimate: 43.9 Å2 / Rmerge(I) obs: 0.162 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.989→3.2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4371 / % possible all: 92.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4QCI Resolution: 2.989→29.735 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.875 / SU B: 49.23 / SU ML: 0.743 / Cross valid method: FREE R-VALUE / ESU R Free: 0.5 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.916 Å2
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Refinement step | Cycle: LAST / Resolution: 2.989→29.735 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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