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- PDB-5ngv: CRYSTAL STRUCTURE OF THE Activin receptor type-2B LIGAND BINDING ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ngv | |||||||||
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Title | CRYSTAL STRUCTURE OF THE Activin receptor type-2B LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV, ORTHORHOMBIC CRYSTAL FORM | |||||||||
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![]() | TRANSFERASE / three-finger toxin fold / antibody Fv fragment | |||||||||
Function / homology | ![]() Regulation of signaling by NODAL / activin receptor activity, type II / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / activin receptor activity / venous blood vessel development / lymphangiogenesis / retina vasculature development in camera-type eye / embryonic foregut morphogenesis / activin receptor complex ...Regulation of signaling by NODAL / activin receptor activity, type II / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / activin receptor activity / venous blood vessel development / lymphangiogenesis / retina vasculature development in camera-type eye / embryonic foregut morphogenesis / activin receptor complex / artery development / receptor protein serine/threonine kinase / activin binding / Signaling by BMP / activin receptor signaling pathway / Signaling by Activin / kinase activator activity / Signaling by NODAL / gastrulation with mouth forming second / pancreas development / determination of left/right symmetry / negative regulation of cold-induced thermogenesis / insulin secretion / skeletal system morphogenesis / anterior/posterior pattern specification / cell surface receptor protein serine/threonine kinase signaling pathway / organ growth / roof of mouth development / growth factor binding / odontogenesis of dentin-containing tooth / mesoderm development / blood vessel remodeling / BMP signaling pathway / positive regulation of osteoblast differentiation / positive regulation of bone mineralization / response to glucose / protein serine/threonine/tyrosine kinase activity / post-embryonic development / kidney development / lung development / cellular response to growth factor stimulus / heart development / receptor complex / protein serine/threonine kinase activity / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
Model details | ORTHORHOMBIC CRYSTAL FORM | |||||||||
![]() | Rondeau, J.-M. / Lehmann, S. | |||||||||
![]() | ![]() Title: Blockade of activin type II receptors with a dual anti-ActRIIA/IIB antibody is critical to promote maximal skeletal muscle hypertrophy. Authors: Morvan, F. / Rondeau, J.-M. / Zou, C. / Minetti, G. / Scheufler, C. / Scharenberg, M. / Jacobi, C. / Brebbia, P. / Ritter, V. / Toussaint, G. / Koelbing, C. / Leber, X. / Schilb, A. / Witte, ...Authors: Morvan, F. / Rondeau, J.-M. / Zou, C. / Minetti, G. / Scheufler, C. / Scharenberg, M. / Jacobi, C. / Brebbia, P. / Ritter, V. / Toussaint, G. / Koelbing, C. / Leber, X. / Schilb, A. / Witte, F. / Lehmann, S. / Koch, E. / Geisse, S. / Glass, D.J. / Lach-Trifilieff, E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 144.3 KB | Display | ![]() |
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PDB format | ![]() | 111.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5nh3C ![]() 5nhrC ![]() 5nhwC ![]() 2h64S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 11646.901 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING domain Source method: isolated from a genetically manipulated source Details: expressed as thioredoxin-His6-fusion protein with a PreScission cleavage site after the His-tag Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q13705, receptor protein serine/threonine kinase |
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#2: Antibody | Mass: 13406.904 Da / Num. of mol.: 1 / Fragment: VH Source method: isolated from a genetically manipulated source Details: periplasmic expression / Source: (gene. exp.) ![]() ![]() ![]() |
#3: Antibody | Mass: 12496.670 Da / Num. of mol.: 1 / Fragment: VL Source method: isolated from a genetically manipulated source Details: periplasmic expression / Source: (gene. exp.) ![]() ![]() ![]() |
#4: Chemical | ChemComp-PG4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.4 / Details: 0.1M PHOSPHATE-CITRATE, 40% PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 14, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→17.05 Å / Num. obs: 28674 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.439 % / Biso Wilson estimate: 33.4 Å2 / Rmerge F obs: 0.146 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.08 / Χ2: 0.956 / Net I/σ(I): 14.23 / Num. measured all: 127273 / Scaling rejects: 10 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2H64 Resolution: 2→17.05 Å / Cor.coef. Fo:Fc: 0.9368 / Cor.coef. Fo:Fc free: 0.9259 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.14 / SU Rfree Blow DPI: 0.122 / SU Rfree Cruickshank DPI: 0.121
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Displacement parameters | Biso max: 144.94 Å2 / Biso mean: 43.57 Å2 / Biso min: 22.35 Å2
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Refine analyze | Luzzati coordinate error obs: 0.224 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→17.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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