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Yorodumi- PDB-6lbm: Crystal Structure of FOXC2-DBD bound to a palindromic DNA sequence -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lbm | ||||||
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Title | Crystal Structure of FOXC2-DBD bound to a palindromic DNA sequence | ||||||
Components |
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Keywords | TRANSCRIPTION / Forkhead transcription / DNA binding specificity | ||||||
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 / embryonic viscerocranium morphogenesis / positive regulation of vascular wound healing / glomerular mesangial cell development / Formation of the ureteric bud / 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 / embryonic viscerocranium morphogenesis / positive regulation of vascular wound healing / glomerular mesangial cell development / Formation of the ureteric bud / podocyte differentiation / lymphangiogenesis / neural crest cell development / regulation of organ growth / metanephros development / embryonic heart tube development / camera-type eye development / collagen fibril organization / positive regulation of cell adhesion mediated by integrin / negative regulation of cold-induced thermogenesis / ventricular cardiac muscle tissue morphogenesis / cardiac muscle cell proliferation / artery morphogenesis / ureteric bud development / DNA-binding transcription activator activity / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / mesoderm development / blood vessel remodeling / anatomical structure morphogenesis / vascular endothelial growth factor receptor signaling pathway / somitogenesis / Notch signaling pathway / positive regulation of endothelial cell migration / blood vessel diameter maintenance / ossification / response to hormone / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.841 Å | ||||||
Authors | Li, J. / Dai, S.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: Mechanism of forkhead transcription factors binding to a novel palindromic DNA site. Authors: Li, J. / Dai, S. / Chen, X. / Liang, X. / Qu, L. / Jiang, L. / Guo, M. / Zhou, Z. / Wei, H. / Zhang, H. / Chen, Z. / Chen, L. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lbm.cif.gz | 92.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lbm.ent.gz | 65.4 KB | Display | PDB format |
PDBx/mmJSON format | 6lbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lbm_validation.pdf.gz | 428.3 KB | Display | wwPDB validaton report |
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Full document | 6lbm_full_validation.pdf.gz | 430.7 KB | Display | |
Data in XML | 6lbm_validation.xml.gz | 7 KB | Display | |
Data in CIF | 6lbm_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/6lbm ftp://data.pdbj.org/pub/pdb/validation_reports/lb/6lbm | HTTPS FTP |
-Related structure data
Related structure data | 6lbiC 6akoS 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: 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 | ||||||
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#2: DNA chain | Mass: 6132.990 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.21 Å3/Da / Density % sol: 70.77 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 50 mM HEPES, pH 7.5, 8%-12% PEG4000 (w/v), 250 mM NaCl, 10 mM MgCl2 and 1 mM TCEP. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→39.281 Å / Num. obs: 9399 / % possible obs: 94.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 71.1 Å2 / CC1/2: 0.986 / Net I/σ(I): 15.43 |
Reflection shell | Resolution: 2.84→2.94 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 547 / CC1/2: 0.718 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6AKO Resolution: 2.841→39.281 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 185.17 Å2 / Biso mean: 82.1874 Å2 / Biso min: 22.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.841→39.281 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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