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Open data
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Basic information
Entry | Database: PDB / ID: 5c4v | ||||||
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Title | Ski-like protein | ||||||
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![]() | SIGNALING PROTEIN / Complex | ||||||
Function / homology | ![]() positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / atrioventricular valve formation / mesendoderm development / activin responsive factor complex / SMAD4 MH2 Domain Mutants in Cancer ...positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / atrioventricular valve formation / mesendoderm development / activin responsive factor complex / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / positive regulation of luteinizing hormone secretion / regulation of hair follicle development / lymphocyte homeostasis / filamin binding / sebaceous gland development / SMAD protein complex / formation of anatomical boundary / epithelial cell migration / RUNX2 regulates bone development / positive regulation of follicle-stimulating hormone secretion / heteromeric SMAD protein complex / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of transforming growth factor beta2 production / neuron fate specification / RUNX3 regulates BCL2L11 (BIM) transcription / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / response to transforming growth factor beta / secondary palate development / FOXO-mediated transcription of cell cycle genes / negative regulation of cardiac muscle hypertrophy / brainstem development / left ventricular cardiac muscle tissue morphogenesis / Transcriptional regulation of pluripotent stem cells / regulation of transforming growth factor beta receptor signaling pathway / atrioventricular canal development / cardiac conduction system development / positive regulation of extracellular matrix assembly / lens fiber cell differentiation / Germ layer formation at gastrulation / sulfate binding / Signaling by BMP / cellular response to BMP stimulus / Formation of definitive endoderm / outflow tract septum morphogenesis / activin receptor signaling pathway / Signaling by Activin / SMAD protein signal transduction / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / response to growth factor / blastocyst formation / Signaling by NODAL / cardiac muscle hypertrophy in response to stress / gastrulation with mouth forming second / I-SMAD binding / neural crest cell differentiation / endothelial cell activation / Cardiogenesis / RUNX3 regulates CDKN1A transcription / embryonic digit morphogenesis / branching involved in ureteric bud morphogenesis / adrenal gland development / positive regulation of axonogenesis / ventricular septum morphogenesis / interleukin-6-mediated signaling pathway / seminiferous tubule development / positive regulation of cardiac muscle cell apoptotic process / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / TGF-beta receptor signaling activates SMADs / R-SMAD binding / negative regulation of cell differentiation / uterus development / positive regulation of SMAD protein signal transduction / negative regulation of BMP signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / developmental growth / single fertilization / epithelial to mesenchymal transition / anatomical structure morphogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / BMP signaling pathway / positive regulation of epithelial to mesenchymal transition / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / extrinsic apoptotic signaling pathway / ovarian follicle development / skeletal muscle tissue development / cellular response to transforming growth factor beta stimulus / collagen binding / ERK1 and ERK2 cascade / transforming growth factor beta receptor signaling pathway / transcription corepressor binding / acrosomal vesicle / response to cytokine / cellular response to glucose stimulus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / axon guidance / negative regulation of transforming growth factor beta receptor signaling pathway Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wallden, K. / Nyman, T. / Hallberg, B.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: SnoN Stabilizes the SMAD3/SMAD4 Protein Complex. Authors: Wallden, K. / Nyman, T. / Hallberg, B.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.1 KB | Display | ![]() |
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PDB format | ![]() | 149.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 497.4 KB | Display | ![]() |
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Full document | ![]() | 510.5 KB | Display | |
Data in XML | ![]() | 33.3 KB | Display | |
Data in CIF | ![]() | 46.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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:
NCS domain segments:
NCS ensembles :
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Components
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 28294.082 Da / Num. of mol.: 3 / Fragment: residues 314-549 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 14617.815 Da / Num. of mol.: 3 / Fragment: residues 238-356 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 136 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GOL / | ||||
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#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2.8-3.3 M sodium chloride, 0.1 M Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 10, 2013 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.6→40.3 Å / Num. obs: 39718 / % possible obs: 97.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 42.5 Å2 / Net I/σ(I): 3.7 | |||||||||||||||
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 0.7 / % possible all: 95.5 |
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Processing
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Refinement | Resolution: 2.6→40.3 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.877 / SU B: 5.86 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.514 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→40.3 Å
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Refine LS restraints |
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