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Yorodumi- PDB-6zmn: Crystal structure of the Smad3-Smad5 MH1 domain chimera bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zmn | |||||||||
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Title | Crystal structure of the Smad3-Smad5 MH1 domain chimera bound to the GGCGC site | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / Smad3 / transcription / TGFbeta / dimerization / hinge loop / protein engineering | |||||||||
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 / sterol response element binding / paraxial mesoderm morphogenesis / 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 / sterol response element binding / paraxial mesoderm morphogenesis / 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 / nuclear glucocorticoid receptor binding / positive regulation of extracellular matrix assembly / 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 / embryonic pattern specification / activin receptor signaling pathway / Signaling by Activin / cell-cell junction organization / Formation of axial mesoderm / SMAD protein signal transduction / Signaling by NODAL / regulation of epithelial cell proliferation / embryonic cranial skeleton morphogenesis / I-SMAD binding / Interleukin-37 signaling / response to angiotensin / positive regulation of positive chemotaxis / osteoblast development / NOTCH4 Intracellular Domain Regulates Transcription / negative regulation of cardiac muscle hypertrophy in response to stress / RUNX3 regulates CDKN1A transcription / nuclear inner membrane / ureteric bud development / negative regulation of fat cell differentiation / DNA-binding transcription repressor activity / adrenal gland development / 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 / regulation of immune response / phosphatase binding / negative regulation of osteoblast differentiation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cis-regulatory region sequence-specific DNA binding / positive regulation of bone mineralization / somitogenesis / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / extrinsic apoptotic signaling pathway / 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 / transcription coactivator binding / negative regulation of protein catabolic process / negative regulation of cell growth / chromatin DNA binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.333 Å | |||||||||
Authors | Pluta, R. / Macias, M.J. | |||||||||
Funding support | Spain, European Union, 2items
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Citation | Journal: Comput Struct Biotechnol J / Year: 2021 Title: Unveiling the dimer/monomer propensities of Smad MH1-DNA complexes. Authors: Ruiz, L. / Kaczmarska, Z. / Gomes, T. / Aragon, E. / Torner, C. / Freier, R. / Baginski, B. / Martin-Malpartida, P. / de Martin Garrido, N. / Marquez, J.A. / Cordeiro, T.N. / Pluta, R. / Macias, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zmn.cif.gz | 150.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zmn.ent.gz | 115.6 KB | Display | PDB format |
PDBx/mmJSON format | 6zmn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/6zmn ftp://data.pdbj.org/pub/pdb/validation_reports/zm/6zmn | HTTPS FTP |
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-Related structure data
Related structure data | 6tbzC 6tceC 5od6S 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
-Protein / DNA chain , 2 types, 4 molecules ABCD
#1: Protein | Mass: 14673.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD3, MADH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P84022 #2: DNA chain | Mass: 4900.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 5 types, 21 molecules
#3: Chemical | ChemComp-ACT / | ||||
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#4: Chemical | ChemComp-EDO / | ||||
#5: Chemical | #6: Chemical | ChemComp-PGE / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 2.84 Å3/Da / Density % sol: 56.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→48.94 Å / Num. obs: 12973 / % possible obs: 91.8 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.37→2.64 Å / Redundancy: 2.9 % / Num. unique obs: 649 / CC1/2: 0.552 / Rpim(I) all: 0.531 / % possible all: 57.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5od6 Resolution: 2.333→26 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.853 / SU R Cruickshank DPI: 0.602 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.649 / SU Rfree Blow DPI: 0.304 / SU Rfree Cruickshank DPI: 0.304
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Displacement parameters | Biso mean: 52.12 Å2
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Refine analyze | Luzzati coordinate error obs: 0.37 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.333→26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.333→3 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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