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- PDB-4s2q: Crystal Structure of HMG domain of the chondrogenesis master regu... -
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Basic information
Entry | Database: PDB / ID: 4s2q | ||||||
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Title | Crystal Structure of HMG domain of the chondrogenesis master regulator, Sox9 in complex with ChIP-Seq identified DNA element | ||||||
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![]() | DNA BINDING PROTEIN/DNA / DNA Bending / Minor groove binding / Transcription Regulation / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() heart valve formation / male germ-line sex determination / epithelial cell proliferation involved in prostatic bud elongation / regulation of cell proliferation involved in tissue homeostasis / regulation of branching involved in lung morphogenesis / morphogenesis of a branching epithelium / renal vesicle induction / metanephric tubule development / ureter urothelium development / positive regulation of kidney development ...heart valve formation / male germ-line sex determination / epithelial cell proliferation involved in prostatic bud elongation / regulation of cell proliferation involved in tissue homeostasis / regulation of branching involved in lung morphogenesis / morphogenesis of a branching epithelium / renal vesicle induction / metanephric tubule development / ureter urothelium development / positive regulation of kidney development / negative regulation of beta-catenin-TCF complex assembly / regulation of epithelial cell proliferation involved in lung morphogenesis / neural crest cell fate specification / ureter smooth muscle cell differentiation / metanephric nephron tubule formation / positive regulation of mesenchymal stem cell differentiation / negative regulation of immune system process / intrahepatic bile duct development / astrocyte fate commitment / bronchus cartilage development / lung smooth muscle development / ureter development / ureter morphogenesis / chondrocyte differentiation involved in endochondral bone morphogenesis / Transcriptional regulation by RUNX2 / negative regulation of fatty acid oxidation / Sertoli cell differentiation / anterior head development / chondrocyte hypertrophy / Harderian gland development / otic vesicle development / retinal rod cell differentiation / cellular response to heparin / growth plate cartilage chondrocyte growth / trachea cartilage development / positive regulation of cell proliferation involved in heart morphogenesis / : / positive regulation of epithelial cell differentiation / chondrocyte development / negative regulation of photoreceptor cell differentiation / regulation of cell cycle process / lacrimal gland development / cochlea morphogenesis / otic vesicle formation / prostate gland morphogenesis / Deactivation of the beta-catenin transactivating complex / positive regulation of male gonad development / positive regulation of cartilage development / intestinal epithelial structure maintenance / negative regulation of mesenchymal cell apoptotic process / endochondral bone morphogenesis / bHLH transcription factor binding / heart valve morphogenesis / positive regulation of chondrocyte differentiation / Sertoli cell development / notochord development / limb bud formation / prostate gland development / neural crest cell development / lung epithelial cell differentiation / negative regulation of bone mineralization / positive regulation of branching involved in ureteric bud morphogenesis / endocrine pancreas development / positive regulation of extracellular matrix assembly / tissue homeostasis / negative regulation of biomineral tissue development / response to fatty acid / cellular response to BMP stimulus / male sex determination / positive regulation of chondrocyte proliferation / mammary gland development / negative regulation of myoblast differentiation / heart valve development / negative regulation of ossification / aortic valve morphogenesis / negative regulation of chondrocyte differentiation / cartilage development / cell fate specification / positive regulation of mesenchymal cell proliferation / endocardial cushion morphogenesis / negative regulation of epithelial cell differentiation / branching involved in ureteric bud morphogenesis / cartilage condensation / epithelial tube branching involved in lung morphogenesis / positive regulation of epithelial cell migration / oligodendrocyte differentiation / regulation of cell differentiation / protein kinase A catalytic subunit binding / somatic stem cell population maintenance / protein localization to nucleus / hair follicle development / epithelial to mesenchymal transition / negative regulation of osteoblast differentiation / cell fate commitment / cellular response to interleukin-1 / cis-regulatory region sequence-specific DNA binding / chondrocyte differentiation / regulation of cell adhesion / pre-mRNA intronic binding / cellular response to retinoic acid Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vivekanandan, S. / Moovarkumudalvan, B. / Lescar, J. / Kolatkar, P.R. | ||||||
![]() | ![]() Title: Crystal Structure of HMG domain of the chondrogenesis master regulator, Sox9 in complex with ChIP-Seq identified DNA element Authors: Vivekanandan, S. / Moovarkumudalvan, B. / Lescar, J. / Kolatkar, P.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.4 KB | Display | ![]() |
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PDB format | ![]() | 60.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.9 KB | Display | ![]() |
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Full document | ![]() | 433.6 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 7.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3f27S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 4871.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 4965.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Protein | Mass: 9264.711 Da / Num. of mol.: 1 / Fragment: UNP residues 103-178 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG 3350, 200mM Sodium/potassium phosphate, 100mM Bis Tris propane, pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2012 |
Radiation | Monochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL SAGITTAL FOCUSING MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 6721 / Num. obs: 6675 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 30.3 % / Rsym value: 0.133 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.7→3.4011 Å / Redundancy: 30.3 % / Mean I/σ(I) obs: 19 / Num. unique all: 6721 / Rsym value: 0.133 / % possible all: 99.9 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3F27 Resolution: 2.7→24.873 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 32.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→24.873 Å
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Refine LS restraints |
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LS refinement shell |
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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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