+Open data
-Basic information
Entry | Database: PDB / ID: 1mr1 | ||||||
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Title | Crystal Structure of a Smad4-Ski Complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Smad / Ski / cancer / TGF-b signaling / protein interaction | ||||||
Function / homology | Function and homology information nose morphogenesis / positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / histone deacetylase inhibitor activity / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / atrioventricular valve formation / somite rostral/caudal axis specification / activin responsive factor complex ...nose morphogenesis / positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / histone deacetylase inhibitor activity / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / atrioventricular valve formation / somite rostral/caudal axis specification / activin responsive factor complex / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / positive regulation of luteinizing hormone secretion / regulation of hair follicle development / myotube differentiation / 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 / regulation of transforming growth factor beta2 production / neuron fate specification / epithelial to mesenchymal transition involved in endocardial cushion formation / filamin binding / RUNX3 regulates BCL2L11 (BIM) transcription / endocardial cell differentiation / response to transforming growth factor beta / secondary palate development / FOXO-mediated transcription of cell cycle genes / lens morphogenesis in camera-type eye / negative regulation of Schwann cell proliferation / brainstem development / negative regulation of cardiac muscle hypertrophy / 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 / Germ layer formation at gastrulation / camera-type eye morphogenesis / sulfate binding / olfactory bulb development / myelination in peripheral nervous system / Signaling by BMP / Formation of definitive endoderm / cellular response to BMP stimulus / activin receptor signaling pathway / outflow tract septum morphogenesis / Signaling by Activin / negative regulation of activin receptor signaling pathway / Signaling by NODAL / camera-type eye development / cardiac muscle hypertrophy in response to stress / SMAD protein signal transduction / gastrulation with mouth forming second / I-SMAD binding / neural crest cell differentiation / bone morphogenesis / endothelial cell activation / face morphogenesis / embryonic limb morphogenesis / Cardiogenesis / RUNX3 regulates CDKN1A transcription / anterior/posterior axis specification / cardiac muscle cell proliferation / branching involved in ureteric bud morphogenesis / adrenal gland development / embryonic digit morphogenesis / ventricular septum morphogenesis / negative regulation of SMAD protein signal transduction / interleukin-6-mediated signaling pathway / roof of mouth development / seminiferous tubule development / positive regulation of cardiac muscle cell apoptotic process / single fertilization / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / TGF-beta receptor signaling activates SMADs / somatic stem cell population maintenance / R-SMAD binding / uterus development / positive regulation of SMAD protein signal transduction / positive regulation of Wnt signaling pathway / negative regulation of BMP signaling pathway / developmental growth / epithelial to mesenchymal transition / anatomical structure morphogenesis / positive regulation of epithelial to mesenchymal transition / negative regulation of osteoblast differentiation / positive regulation of DNA binding / BMP signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / skeletal muscle fiber development / negative regulation of fibroblast proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / extrinsic apoptotic signaling pathway Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Wu, J.-W. / Krawitz, A.R. / Chai, J. / Li, W. / Zhang, F. / Luo, K. / Shi, Y. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2002 Title: Structural Mechanism of Smad4 Recognition by the Nuclear Oncoprotein Ski: Insights on Ski-mediated Repression of TGF-beta Signaling Authors: Wu, J.-W. / Krawitz, A.R. / Chai, J. / Li, W. / Zhang, F. / Luo, K. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mr1.cif.gz | 123.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mr1.ent.gz | 95.9 KB | Display | PDB format |
PDBx/mmJSON format | 1mr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/1mr1 ftp://data.pdbj.org/pub/pdb/validation_reports/mr/1mr1 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25642.287 Da / Num. of mol.: 2 / Fragment: MH2 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q13485 #2: Protein | Mass: 11519.203 Da / Num. of mol.: 2 / Fragment: Smad4-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P12755 #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 3.3 Å3/Da / Density % sol: 62.75 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: dioxane, potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: used macroseeding | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Nov 15, 2001 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→99 Å / Num. all: 23957 / Num. obs: 22639 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.85→2.95 Å / % possible all: 61 |
Reflection | *PLUS Lowest resolution: 99 Å / Redundancy: 6.1 % / Num. measured all: 136326 / Rmerge(I) obs: 0.073 |
Reflection shell | *PLUS % possible obs: 61.2 % / Rmerge(I) obs: 0.457 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→20 Å / σ(F): 0.5 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.85→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.28 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |