+Open data
-Basic information
Entry | Database: PDB / ID: 5mez | ||||||
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Title | Crystal structure of Smad4-MH1 bound to the GGCT site. | ||||||
Components |
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Keywords | TRANSCRIPTION / Smads / transcription factor / DNA complex | ||||||
Function / homology | Function and homology information positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / atrioventricular valve formation / activin responsive factor complex / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer ...positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / atrioventricular valve formation / 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 / 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 / filamin binding / epithelial to mesenchymal transition involved in endocardial cushion formation / RUNX3 regulates BCL2L11 (BIM) transcription / endocardial cell differentiation / response to transforming growth factor beta / secondary palate development / FOXO-mediated transcription of cell cycle genes / negative regulation of cardiac muscle hypertrophy / brainstem development / 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 / sulfate binding / Signaling by BMP / Formation of definitive endoderm / cellular response to BMP stimulus / activin receptor signaling pathway / outflow tract septum morphogenesis / Signaling by Activin / SMAD protein signal transduction / Signaling by NODAL / cardiac muscle hypertrophy in response to stress / gastrulation with mouth forming second / I-SMAD binding / neural crest cell differentiation / endothelial cell activation / Cardiogenesis / RUNX3 regulates CDKN1A transcription / branching involved in ureteric bud morphogenesis / embryonic digit morphogenesis / adrenal gland development / ventricular septum morphogenesis / interleukin-6-mediated signaling pathway / seminiferous tubule development / positive regulation of cardiac muscle cell apoptotic process / positive regulation of transforming growth factor beta receptor signaling pathway / TGF-beta receptor signaling activates SMADs / single fertilization / R-SMAD binding / uterus development / positive regulation of SMAD protein signal transduction / developmental growth / anatomical structure morphogenesis / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / BMP signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / ovarian follicle development / extrinsic apoptotic signaling pathway / ERK1 and ERK2 cascade / cellular response to transforming growth factor beta stimulus / collagen binding / transforming growth factor beta receptor signaling pathway / transcription corepressor binding / axon guidance / cellular response to glucose stimulus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of canonical Wnt signaling pathway / transcription coactivator binding / negative regulation of cell growth / negative regulation of ERK1 and ERK2 cascade / negative regulation of protein catabolic process / osteoblast differentiation / positive regulation of miRNA transcription / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / cell population proliferation / intracellular iron ion homeostasis / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å | ||||||
Authors | Kaczmarska, Z. / Freier, R. / Marquez, J.A. / Macias, M.J. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors. Authors: Martin-Malpartida, P. / Batet, M. / Kaczmarska, Z. / Freier, R. / Gomes, T. / Aragon, E. / Zou, Y. / Wang, Q. / Xi, Q. / Ruiz, L. / Vea, A. / Marquez, J.A. / Massague, J. / 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 | 5mez.cif.gz | 114.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mez.ent.gz | 80.8 KB | Display | PDB format |
PDBx/mmJSON format | 5mez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/5mez ftp://data.pdbj.org/pub/pdb/validation_reports/me/5mez | HTTPS FTP |
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-Related structure data
Related structure data | 5meyC 5mf0C 5nm9C 5od6C 5odgC 3qsvS S: Starting model for refinement C: citing same article (ref.) |
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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: 15237.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD4, DPC4, MADH4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13485 #2: DNA chain | Mass: 4899.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: Chemical | #4: Chemical | ChemComp-CL / | #5: 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: 3.63 Å3/Da / Density % sol: 66.12 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 24% PEG 3350, 0.2 M calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 31, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→30 Å / Num. obs: 12239 / % possible obs: 99.7 % / Redundancy: 3.83 % / Biso Wilson estimate: 90.22 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.094 / Net I/σ(I): 12.86 |
Reflection shell | Resolution: 2.98→2.99 Å / Redundancy: 4.06 % / Mean I/σ(I) obs: 1.68 / Num. measured obs: 459 / Num. unique all: 113 / CC1/2: 0.699 / Rrim(I) all: 0.915 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QSV Resolution: 2.98→29.05 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.888 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.705 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.775 / SU Rfree Blow DPI: 0.343 / SU Rfree Cruickshank DPI: 0.341
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Displacement parameters | Biso mean: 80.41 Å2
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Refine analyze | Luzzati coordinate error obs: 0.43 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.98→29.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.98→3.26 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
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Refinement TLS params. | L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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