[English] 日本語
Yorodumi- PDB-4xrm: homodimer of TALE type homeobox transcription factor MEIS1 comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xrm | ||||||
---|---|---|---|---|---|---|---|
Title | homodimer of TALE type homeobox transcription factor MEIS1 complexes with specific DNA | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / TALE homeobox / MEIS / Complex / DNA | ||||||
Function / homology | Function and homology information positive regulation of cardiac muscle myoblast proliferation / negative regulation of myeloid cell differentiation / eye development / embryonic pattern specification / response to growth factor / pancreas development / transcription factor binding / response to mechanical stimulus / positive regulation of mitotic cell cycle / animal organ morphogenesis ...positive regulation of cardiac muscle myoblast proliferation / negative regulation of myeloid cell differentiation / eye development / embryonic pattern specification / response to growth factor / pancreas development / transcription factor binding / response to mechanical stimulus / positive regulation of mitotic cell cycle / animal organ morphogenesis / visual learning / brain development / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of cell population proliferation / chromatin / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Morgunova, E. / Jorma, A. / Yin, Y. / Nitta, K.R. / Dave, K. / Enge, M. / Kivioja, T. / Popov, A. / Taipale, J. | ||||||
Citation | Journal: Nature / Year: 2015 Title: DNA-dependent formation of transcription factor pairs alters their binding specificity. Authors: Jolma, A. / Yin, Y. / Nitta, K.R. / Dave, K. / Popov, A. / Taipale, M. / Enge, M. / Kivioja, T. / Morgunova, E. / Taipale, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4xrm.cif.gz | 132.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4xrm.ent.gz | 101.9 KB | Display | PDB format |
PDBx/mmJSON format | 4xrm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xrm_validation.pdf.gz | 461.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4xrm_full_validation.pdf.gz | 462.7 KB | Display | |
Data in XML | 4xrm_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 4xrm_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/4xrm ftp://data.pdbj.org/pub/pdb/validation_reports/xr/4xrm | HTTPS FTP |
-Related structure data
Related structure data | 4xrsC 5bngC 3k2aS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 5236.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
---|---|---|---|---|---|
#2: DNA chain | Mass: 5178.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
#3: Protein | Mass: 7517.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MEIS2, MRG1 / Plasmid: PETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 pLysS / References: UniProt: O14770 #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.08 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PME 5000, Tris, PEG 400, magnesium chloride / PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2014 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. all: 149060 / Num. obs: 36011 / % possible obs: 97.28 % / Redundancy: 4.1 % / Biso Wilson estimate: 25.92 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 14.84 |
Reflection shell | Resolution: 1.6→1.657 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.7128 / Mean I/σ(I) obs: 1.56 / % possible all: 93.87 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3k2a Resolution: 1.6→19.83 Å / FOM work R set: 0.7632 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.74 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 196.26 Å2 / Biso mean: 42.14 Å2 / Biso min: 20.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→19.83 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|