+Open data
-Basic information
Entry | Database: PDB / ID: 6ako | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of FOXC2 DBD Bound to DBE2 DNA | |||||||||
Components |
| |||||||||
Keywords | DNA BINDING PROTEIN/DNA / FOXC / DNA binding domain / DNA recognition / Crystal Structure / Lymphoedema distichiasis syndrome / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information apoptotic process involved in outflow tract morphogenesis / negative regulation of apoptotic process involved in outflow tract morphogenesis / paraxial mesodermal cell fate commitment / glomerular endothelium development / Formation of intermediate mesoderm / positive regulation of vascular wound healing / embryonic viscerocranium morphogenesis / lymphangiogenesis / glomerular mesangial cell development / podocyte differentiation ...apoptotic process involved in outflow tract morphogenesis / negative regulation of apoptotic process involved in outflow tract morphogenesis / paraxial mesodermal cell fate commitment / glomerular endothelium development / Formation of intermediate mesoderm / positive regulation of vascular wound healing / embryonic viscerocranium morphogenesis / lymphangiogenesis / glomerular mesangial cell development / podocyte differentiation / neural crest cell development / regulation of organ growth / metanephros development / camera-type eye development / embryonic heart tube development / artery morphogenesis / collagen fibril organization / negative regulation of cold-induced thermogenesis / positive regulation of cell adhesion mediated by integrin / ureteric bud development / cardiac muscle cell proliferation / ventricular cardiac muscle tissue morphogenesis / branching involved in blood vessel morphogenesis / DNA-binding transcription activator activity / positive regulation of cell migration involved in sprouting angiogenesis / mesoderm development / anatomical structure morphogenesis / blood vessel remodeling / vascular endothelial growth factor receptor signaling pathway / somitogenesis / Notch signaling pathway / blood vessel diameter maintenance / ossification / response to hormone / positive regulation of endothelial cell migration / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / chromatin DNA binding / sequence-specific double-stranded DNA binding / insulin receptor signaling pathway / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / cell differentiation / nuclear body / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.396 Å | |||||||||
Authors | Chen, X. / Wei, H. / Li, J. / Liang, X. / Dai, S. / Jiang, L. / Guo, M. / Chen, Y. | |||||||||
Funding support | China, 2items
| |||||||||
Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Structural basis for DNA recognition by FOXC2. Authors: Chen, X. / Wei, H. / Li, J. / Liang, X. / Dai, S. / Jiang, L. / Guo, M. / Qu, L. / Chen, Z. / Chen, L. / Chen, Y. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ako.cif.gz | 94.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ako.ent.gz | 67.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ako.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/6ako ftp://data.pdbj.org/pub/pdb/validation_reports/ak/6ako | HTTPS FTP |
---|
-Related structure data
Related structure data | 6akpC 5x07S 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: 4932.272 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
---|---|
#2: DNA chain | Mass: 4860.159 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#3: Protein | Mass: 12330.169 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FOXC2, FKHL14, MFH1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99958 |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.57 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 50 mM Bis-Tris propane (pH 6.68), 14% PEG4K, 200 mM NaCl, 10 mM MgCl2, 1 mM TCEP |
-Data collection
Diffraction | Mean temperature: 85 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.587 Å |
Detector | Type: RIGAKU / Detector: CCD / Date: Mar 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.587 Å / Relative weight: 1 |
Reflection | Resolution: 2.396→40.97 Å / Num. obs: 11726 / % possible obs: 92 % / Redundancy: 12.1 % / CC1/2: 1 / Rmerge(I) obs: 0.04052 / Net I/σ(I): 34.65 |
Reflection shell | Resolution: 2.396→2.482 Å / Rmerge(I) obs: 0.3016 / Num. unique obs: 780 / CC1/2: 0.979 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5X07 Resolution: 2.396→40.97 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.5
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.396→40.97 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|