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Yorodumi- PDB-6fqp: Crystal structure of TALE homeobox domain transcription factor TG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fqp | |||||||||
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Title | Crystal structure of TALE homeobox domain transcription factor TGIF1 with its consensus DNA | |||||||||
Components |
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Keywords | TRANSCRIPTION / homeobox / three-amino acid loop extension / TGF-beta pathway | |||||||||
Function / homology | Function and homology information co-SMAD binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / cellular response to growth factor stimulus / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity ...co-SMAD binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / cellular response to growth factor stimulus / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | |||||||||
Authors | Guca, E. / Macias, M.J. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: TGIF1 homeodomain interacts with Smad MH1 domain and represses TGF-beta signaling. Authors: Guca, E. / Sunol, D. / Ruiz, L. / Konkol, A. / Cordero, J. / Torner, C. / Aragon, E. / Martin-Malpartida, P. / Riera, A. / 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 | 6fqp.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fqp.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/6fqp ftp://data.pdbj.org/pub/pdb/validation_reports/fq/6fqp | HTTPS FTP |
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-Related structure data
Related structure data | 6fqqC 4xrmS 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: DNA chain | Mass: 4897.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #2: Protein | Mass: 11729.339 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal 'GP' sequence comes from the purification tag Source: (gene. exp.) Homo sapiens (human) / Gene: TGIF1, TGIF / Production host: Escherichia coli (E. coli) / References: UniProt: Q15583 #3: Chemical | ChemComp-CA / | #4: 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: 3.39 Å3/Da / Density % sol: 63.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium acetate trihydrate pH 4.5, 30% v/v PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972422 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972422 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→67.25 Å / Num. obs: 13814 / % possible obs: 98.9 % / Redundancy: 2 % / Rmerge(I) obs: 0.0275 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.42→2.51 Å / Rmerge(I) obs: 0.232 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XRM Resolution: 2.42→45.537 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||
Displacement parameters | Biso max: 117.63 Å2 / Biso mean: 52.9948 Å2 / Biso min: 23.84 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.42→45.537 Å
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