+Open data
-Basic information
Entry | Database: PDB / ID: 1ozj | ||||||
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Title | Crystal structure of Smad3-MH1 bound to DNA at 2.4 A resolution | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / Smad / Mad homology domain 1 / DNA recognition / TGF-beta signaling / zinc-binding module / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of transforming growth factor beta3 production / transdifferentiation / paraxial mesoderm morphogenesis / sterol response element binding / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway ...nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of transforming growth factor beta3 production / transdifferentiation / paraxial mesoderm morphogenesis / sterol response element binding / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / regulation of striated muscle tissue development / SMAD protein complex / immune system development / co-SMAD binding / heteromeric SMAD protein complex / regulation of transforming growth factor beta2 production / RUNX3 regulates BCL2L11 (BIM) transcription / DEAD/H-box RNA helicase binding / bHLH transcription factor binding / pericardium development / FOXO-mediated transcription of cell cycle genes / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of chondrocyte differentiation / negative regulation of osteoblast proliferation / regulation of transforming growth factor beta receptor signaling pathway / embryonic foregut morphogenesis / negative regulation of wound healing / lens fiber cell differentiation / positive regulation of extracellular matrix assembly / nuclear glucocorticoid receptor binding / transforming growth factor beta receptor binding / primary miRNA processing / Germ layer formation at gastrulation / endoderm development / signal transduction involved in regulation of gene expression / Formation of definitive endoderm / cell-cell junction organization / embryonic pattern specification / activin receptor signaling pathway / Signaling by Activin / Formation of axial mesoderm / Signaling by NODAL / embryonic cranial skeleton morphogenesis / regulation of epithelial cell proliferation / SMAD protein signal transduction / I-SMAD binding / Interleukin-37 signaling / response to angiotensin / positive regulation of positive chemotaxis / osteoblast development / RUNX3 regulates CDKN1A transcription / NOTCH4 Intracellular Domain Regulates Transcription / nuclear inner membrane / negative regulation of cardiac muscle hypertrophy in response to stress / ureteric bud development / negative regulation of fat cell differentiation / adrenal gland development / DNA-binding transcription repressor activity / negative regulation of cytosolic calcium ion concentration / heart looping / TGF-beta receptor signaling activates SMADs / positive regulation of focal adhesion assembly / R-SMAD binding / thyroid gland development / mesoderm formation / developmental growth / anatomical structure morphogenesis / positive regulation of epithelial to mesenchymal transition / negative regulation of osteoblast differentiation / regulation of immune response / phosphatase binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cis-regulatory region sequence-specific DNA binding / positive regulation of bone mineralization / somitogenesis / extrinsic apoptotic signaling pathway / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / JNK cascade / positive regulation of stress fiber assembly / cellular response to transforming growth factor beta stimulus / collagen binding / T cell activation / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / transcription corepressor binding / negative regulation of miRNA transcription / liver development / ubiquitin binding / positive regulation of interleukin-1 beta production / promoter-specific chromatin binding / nuclear receptor binding / cellular response to glucose stimulus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / wound healing / negative regulation of protein catabolic process / transcription coactivator binding / negative regulation of cell growth / chromatin DNA binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Chai, J. / Wu, J.-W. / Yan, N. / Massague, J. / Pavletich, N.P. / Shi, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Features of a Smad3 MH1-DNA complex. Roles of water and zinc in DNA binding. Authors: Chai, J. / Wu, J.-W. / Yan, N. / Massague, J. / Pavletich, N.P. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ozj.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ozj.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ozj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/1ozj ftp://data.pdbj.org/pub/pdb/validation_reports/oz/1ozj | 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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Unit cell |
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-Components
#1: DNA chain | Mass: 4552.986 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
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#2: DNA chain | Mass: 4624.021 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
#3: Protein | Mass: 16847.787 Da / Num. of mol.: 2 / Fragment: DWA DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MADH3 OR SMAD3 OR MAD3 / Production host: Escherichia coli (E. coli) / References: UniProt: P84022 #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.87 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: citrate, PEG2000, ammonium acetate, spermine, magnesium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Shi, Y., (1998) Cell, 94, 585. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 2002 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→99 Å / Num. all: 14974 / Num. obs: 14360 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.4→2.5 Å / % possible all: 82.5 |
Reflection | *PLUS Lowest resolution: 99 Å / Redundancy: 4.8 % / Num. measured all: 68907 / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 82.5 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 5.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→15 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rfree: 0.27 / Rfactor Rwork: 0.212 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.265 |