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Open data
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Basic information
Entry | Database: PDB / ID: 7cd1 | ||||||
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Title | Crystal structure of inhibitory Smad, Smad7 | ||||||
![]() | Mothers against decapentaplegic homolog 7 | ||||||
![]() | SIGNALING PROTEIN / MH2 domain / Smad / TGF-BETA / SIGNAL TRANSDUCTION | ||||||
Function / homology | ![]() : / regulation of activin receptor signaling pathway / protein-containing complex localization => GO:0031503 / : / positive regulation of chondrocyte hypertrophy / negative regulation of T-helper 17 type immune response / Signaling by BMP / negative regulation of chondrocyte proliferation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Downregulation of TGF-beta receptor signaling ...: / regulation of activin receptor signaling pathway / protein-containing complex localization => GO:0031503 / : / positive regulation of chondrocyte hypertrophy / negative regulation of T-helper 17 type immune response / Signaling by BMP / negative regulation of chondrocyte proliferation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Downregulation of TGF-beta receptor signaling / negative regulation of T cell cytokine production / heteromeric SMAD protein complex / regulation of ventricular cardiac muscle cell membrane depolarization / positive regulation of cell-cell adhesion / negative regulation of T-helper 17 cell differentiation / response to laminar fluid shear stress / regulation of epithelial to mesenchymal transition / regulation of transforming growth factor beta receptor signaling pathway / negative regulation of transcription by competitive promoter binding / negative regulation of ubiquitin-protein transferase activity / activin binding / type I transforming growth factor beta receptor binding / adherens junction assembly / SMAD protein signal transduction / Ub-specific processing proteases / catenin complex / I-SMAD binding / negative regulation of ossification / transcription regulator inhibitor activity / ventricular cardiac muscle tissue morphogenesis / artery morphogenesis / ureteric bud development / ventricular septum morphogenesis / negative regulation of peptidyl-threonine phosphorylation / negative regulation of peptidyl-serine phosphorylation / transcription factor binding / negative regulation of BMP signaling pathway / regulation of cardiac muscle contraction / anatomical structure morphogenesis / BMP signaling pathway / negative regulation of protein ubiquitination / cellular response to transforming growth factor beta stimulus / collagen binding / transforming growth factor beta receptor signaling pathway / positive regulation of protein ubiquitination / cellular response to leukemia inhibitory factor / adherens junction / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of DNA-binding transcription factor activity / fibrillar center / beta-catenin binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / protein stabilization / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / centrosome / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Murayama, K. / Kato-Murayama, M. / Shirouzu, M. | ||||||
![]() | ![]() Title: Structural basis for inhibitory effects of Smad7 on TGF-beta family signaling. Authors: Murayama, K. / Kato-Murayama, M. / Itoh, Y. / Miyazono, K. / Miyazawa, K. / Shirouzu, 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 | ![]() | 186.3 KB | Display | ![]() |
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PDB format | ![]() | 135.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.2 KB | Display | ![]() |
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Full document | ![]() | 484 KB | Display | |
Data in XML | ![]() | 33.3 KB | Display | |
Data in CIF | ![]() | 47.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1khxS S: Starting model for refinement |
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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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Components
#1: Protein | Mass: 21468.221 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: Na Citrate, MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Dec 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→50 Å / Num. obs: 71133 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.128 / Net I/σ(I): 19.38 |
Reflection shell | Resolution: 1.9→1.97 Å / Num. unique obs: 7017 / CC1/2: 0.879 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KHX Resolution: 1.89→36.5 Å / SU ML: 0.1819 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.1392 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→36.5 Å
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Refine LS restraints |
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LS refinement shell |
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