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Yorodumi- PDB-4euw: Crystal structure of a HMG domain of transcription factor SOX-9 b... -
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-Basic information
Entry | Database: PDB / ID: 4euw | ||||||
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Title | Crystal structure of a HMG domain of transcription factor SOX-9 bound to DNA (SOX-9/DNA) from Homo sapiens at 2.77 A resolution | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / HMG DOMAIN / ACTIVATOR / DNA-BINDING / NUCLEUS / TRANSCRIPTION / TRANSCRIPTION REGULATION / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for Stem Cell Biology / STEMCELL / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information 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 / ureter urothelium development / positive regulation of kidney development / negative regulation of beta-catenin-TCF complex assembly ...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 / 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 morphogenesis / chondrocyte differentiation involved in endochondral bone morphogenesis / negative regulation of fatty acid oxidation / Sertoli cell differentiation / anterior head development / chondrocyte hypertrophy / Harderian gland 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 / negative regulation of photoreceptor cell differentiation / regulation of cell cycle process / lacrimal gland development / cochlea morphogenesis / otic vesicle formation / positive regulation of male gonad development / positive regulation of cartilage development / intestinal epithelial structure maintenance / negative regulation of mesenchymal cell apoptotic process / bHLH transcription factor binding / positive regulation of chondrocyte differentiation / prostate gland development / Sertoli cell development / heart valve morphogenesis / notochord development / limb bud formation / neural crest cell development / chromatin => GO:0000785 / lung epithelial cell differentiation / negative regulation of bone mineralization / endocrine pancreas development / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of extracellular matrix assembly / Transcriptional regulation by RUNX2 / tissue homeostasis / negative regulation of biomineral tissue development / response to fatty acid / cellular response to BMP stimulus / 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 / hair follicle development / 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 / negative regulation of osteoblast differentiation / positive regulation of epithelial cell migration / oligodendrocyte differentiation / protein kinase A catalytic subunit binding / somatic stem cell population maintenance / cellular response to epidermal growth factor stimulus / protein localization to nucleus / cellular response to interleukin-1 / epithelial to mesenchymal transition / cis-regulatory region sequence-specific DNA binding / chondrocyte differentiation / regulation of cell adhesion / ossification / pre-mRNA intronic binding / cellular response to retinoic acid / positive regulation of epithelial cell proliferation / negative regulation of miRNA transcription / Notch signaling pathway / cytoskeleton organization / cellular response to transforming growth factor beta stimulus / ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.77 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology (STEMCELL) | ||||||
Citation | Journal: To be published Title: Crystal structure of a HMG domain of transcription factor SOX-9 bound to DNA (SOX-9/DNA) from Homo sapiens at 2.77 A resolution Authors: Joint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4euw.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4euw.ent.gz | 50.9 KB | Display | PDB format |
PDBx/mmJSON format | 4euw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4euw_validation.pdf.gz | 430.1 KB | Display | wwPDB validaton report |
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Full document | 4euw_full_validation.pdf.gz | 430.1 KB | Display | |
Data in XML | 4euw_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 4euw_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/4euw ftp://data.pdbj.org/pub/pdb/validation_reports/eu/4euw | HTTPS FTP |
-Related structure data
Related structure data | 3f27S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 12917.722 Da / Num. of mol.: 1 / Fragment: HMG box containing residues 98-181 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SGT82680, SOX9 / Plasmid: pRSF2Ek6TevLIC / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3)PhageR20080807 / References: UniProt: P48436 |
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#2: DNA chain | Mass: 3677.415 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: sequence matching the SOX-9 binding site from the anti-Mullerian hormone (AMH) promoter, top strand Source: (synth.) Homo sapiens (human) |
#3: DNA chain | Mass: 3646.405 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: sequence matching the SOX-9 binding site from the anti-Mullerian hormone (AMH) promoter, bottom strand Source: (synth.) Homo sapiens (human) |
#4: Water | ChemComp-HOH / |
Sequence details | THIS CONSTRUCT (RESIDUES 98 - 181) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 30.00% polyethylene glycol 8000, 0.20M ammonium acetate, 0.010 M magnesium acetate, 0.1M sodium cacodylate pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 21, 2011 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.77→27.922 Å / Num. obs: 4880 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 86.94 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.3 / Num. measured all: 18522 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F27 Resolution: 2.77→27.92 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 1 / SU B: 34.503 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R: 1.261 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM TLS ASSIGNMENT. 4. REFMAC JELLY-MODEL (RIDGE - 0.02) RESTRAINTS WERE INCLUDED. 5. B-FACTOR WEIGHTING WAS 1.0 2.0 3.0 2.0 3.0.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2.77→27.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.77→2.841 Å / Total num. of bins used: 20
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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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