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- PDB-5nh3: CRYSTAL STRUCTURE OF THE Activin receptor type-2A LIGAND BINDING ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nh3 | ||||||||||||
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Title | CRYSTAL STRUCTURE OF THE Activin receptor type-2A LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV | ||||||||||||
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![]() | TRANSFERASE / OTHER / EPITOPE MAPPING | ||||||||||||
Function / homology | ![]() Regulation of signaling by NODAL / inhibin-betaglycan-ActRII complex / inhibin binding / penile erection / positive regulation of activin receptor signaling pathway / activin receptor activity / Sertoli cell proliferation / sperm ejaculation / BMP receptor activity / embryonic skeletal system development ...Regulation of signaling by NODAL / inhibin-betaglycan-ActRII complex / inhibin binding / penile erection / positive regulation of activin receptor signaling pathway / activin receptor activity / Sertoli cell proliferation / sperm ejaculation / BMP receptor activity / embryonic skeletal system development / activin receptor complex / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / Signaling by BMP / activin binding / cellular response to BMP stimulus / activin receptor signaling pathway / Signaling by Activin / Signaling by NODAL / gastrulation with mouth forming second / regulation of nitric oxide biosynthetic process / determination of left/right symmetry / anterior/posterior pattern specification / cell surface receptor protein serine/threonine kinase signaling pathway / growth factor binding / odontogenesis of dentin-containing tooth / mesoderm development / positive regulation of SMAD protein signal transduction / positive regulation of bone mineralization / BMP signaling pathway / positive regulation of osteoblast differentiation / coreceptor activity / positive regulation of erythrocyte differentiation / PDZ domain binding / cellular response to growth factor stimulus / : / spermatogenesis / receptor complex / positive regulation of protein phosphorylation / phosphorylation / protein serine/threonine kinase activity / cell surface / positive regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Scheufler, C. | ||||||||||||
![]() | ![]() 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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Download
PDBx/mmCIF format | ![]() | 267.5 KB | Display | ![]() |
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PDB format | ![]() | 214.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 799.5 KB | Display | ![]() |
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Full document | ![]() | 801.4 KB | Display | |
Data in XML | ![]() | 27.6 KB | Display | |
Data in CIF | ![]() | 39.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ngvSC ![]() 5nhrC ![]() 5nhwC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Antibody , 2 types, 4 molecules HILM
#2: Antibody | Mass: 13406.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Antibody | Mass: 12513.700 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Protein / Non-polymers , 2 types, 363 molecules AB![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#1: Protein | Mass: 14196.831 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P27037, receptor protein serine/threonine kinase #6: Water | ChemComp-HOH / | |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium citrate tribasic dihydrate pH3.5 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99992 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 38338 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 45.93 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.2 / % possible all: 97.3 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 5NGV Resolution: 2.35→47.55 Å / Cor.coef. Fo:Fc: 0.9448 / Cor.coef. Fo:Fc free: 0.9248 / SU R Cruickshank DPI: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.22 / SU Rfree Blow DPI: 0.182 / SU Rfree Cruickshank DPI: 0.182
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Displacement parameters | Biso mean: 39.78 Å2
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Refine analyze | Luzzati coordinate error obs: 0.245 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→47.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.41 Å / Total num. of bins used: 19
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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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