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Yorodumi- PDB-1u7f: Crystal Structure of the phosphorylated Smad3/Smad4 heterotrimeri... -
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-Basic information
Entry | Database: PDB / ID: 1u7f | ||||||
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Title | Crystal Structure of the phosphorylated Smad3/Smad4 heterotrimeric complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Smad / TGF-beta / signal transduction / protein complex / phosphorylation | ||||||
Function / homology | Function and homology information nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / positive regulation of transforming growth factor beta3 production / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification ...nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / positive regulation of transforming growth factor beta3 production / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / sterol response element binding / paraxial mesoderm morphogenesis / atrioventricular valve formation / transdifferentiation / activin responsive factor complex / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / regulation of hair follicle development / regulation of striated muscle tissue development / filamin binding / sebaceous gland development / positive regulation of luteinizing hormone secretion / SMAD protein complex / formation of anatomical boundary / negative regulation of cardiac muscle hypertrophy in response to stress / immune system development / epithelial cell migration / RUNX2 regulates bone development / heteromeric SMAD protein complex / regulation of transforming growth factor beta2 production / co-SMAD binding / positive regulation of follicle-stimulating hormone secretion / neuron fate specification / RUNX3 regulates BCL2L11 (BIM) transcription / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / DEAD/H-box RNA helicase binding / response to transforming growth factor beta / bHLH transcription factor binding / secondary palate development / pericardium development / FOXO-mediated transcription of cell cycle genes / regulation of transforming growth factor beta receptor signaling pathway / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of chondrocyte differentiation / negative regulation of osteoblast proliferation / negative regulation of cardiac muscle hypertrophy / brainstem development / left ventricular cardiac muscle tissue morphogenesis / Transcriptional regulation of pluripotent stem cells / embryonic foregut morphogenesis / atrioventricular canal development / negative regulation of wound healing / cardiac conduction system development / nuclear glucocorticoid receptor binding / positive regulation of extracellular matrix assembly / lens fiber cell differentiation / primary miRNA processing / transforming growth factor beta receptor binding / Germ layer formation at gastrulation / sulfate binding / Signaling by BMP / cellular response to BMP stimulus / endoderm development / Formation of definitive endoderm / embryonic pattern specification / outflow tract septum morphogenesis / signal transduction involved in regulation of gene expression / activin receptor signaling pathway / SMAD protein signal transduction / Signaling by Activin / Formation of axial mesoderm / cell-cell junction organization / Signaling by NODAL / regulation of epithelial cell proliferation / cardiac muscle hypertrophy in response to stress / embryonic cranial skeleton morphogenesis / R-SMAD binding / gastrulation with mouth forming second / I-SMAD binding / Interleukin-37 signaling / response to angiotensin / neural crest cell differentiation / endothelial cell activation / positive regulation of positive chemotaxis / Cardiogenesis / osteoblast development / nuclear inner membrane / RUNX3 regulates CDKN1A transcription / NOTCH4 Intracellular Domain Regulates Transcription / ureteric bud development / DNA-binding transcription repressor activity / embryonic digit morphogenesis / branching involved in ureteric bud morphogenesis / adrenal gland development / negative regulation of osteoblast differentiation / ventricular septum morphogenesis Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Chacko, B.M. / Qin, B.Y. / Tiwari, A. / Shi, G. / Lam, S. / Hayward, L.J. / de Caestecker, M. / Lin, K. | ||||||
Citation | Journal: Mol.Cell / Year: 2004 Title: Structural basis of heteromeric smad protein assembly in tgf-Beta signaling Authors: Chacko, B.M. / Qin, B.Y. / Tiwari, A. / Shi, G. / Lam, S. / Hayward, L.J. / De Caestecker, M. / Lin, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u7f.cif.gz | 137.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u7f.ent.gz | 107 KB | Display | PDB format |
PDBx/mmJSON format | 1u7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1u7f_validation.pdf.gz | 457.6 KB | Display | wwPDB validaton report |
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Full document | 1u7f_full_validation.pdf.gz | 493 KB | Display | |
Data in XML | 1u7f_validation.xml.gz | 31.3 KB | Display | |
Data in CIF | 1u7f_validation.cif.gz | 42.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u7/1u7f ftp://data.pdbj.org/pub/pdb/validation_reports/u7/1u7f | HTTPS FTP |
-Related structure data
Related structure data | 1u7vC 1khxS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22467.271 Da / Num. of mol.: 2 / Fragment: MH2 and Linker domains Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD3, MADH3 / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P84022 #2: Protein | | Mass: 26060.693 Da / Num. of mol.: 1 / Fragment: MH2 and Linker domains Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD4, MADH4, DPC4 / Plasmid: pGEX-4T2 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q13485 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50 mM Tris-HCl, 0-15 mM magnesium chloride, 5-15% ethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.5→100 Å / Num. all: 21793 / Num. obs: 20128 / % possible obs: 92.4 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 27.5 | ||||||||||||||||||
Reflection shell | Resolution: 2.5→2.6 Å / Mean I/σ(I) obs: 3 / Num. unique all: 1110 / % possible all: 87.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KHX Resolution: 2.6→100 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 64 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.69 Å
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