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- PDB-3us0: Structure of p63 DNA Binding Domain in Complex with a 22 Base Pai... -
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Basic information
Entry | Database: PDB / ID: 3us0 | ||||||
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Title | Structure of p63 DNA Binding Domain in Complex with a 22 Base Pair A/T Rich Response Element Containing a Two Base Pair "AT" Spacer Between Half Sites | ||||||
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![]() | TRANSCRIPTION ACTIVATOR/DNA / B-DNA double helix / zinc binding / beta sandwich / Greek key / transcription factor / nucleus / TRANSCRIPTION ACTIVATOR-DNA complex | ||||||
Function / homology | ![]() ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / prostatic bud formation / negative regulation of mesoderm development / female genitalia morphogenesis / establishment of planar polarity / positive regulation of keratinocyte proliferation / negative regulation of keratinocyte differentiation ...ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / prostatic bud formation / negative regulation of mesoderm development / female genitalia morphogenesis / establishment of planar polarity / positive regulation of keratinocyte proliferation / negative regulation of keratinocyte differentiation / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / polarized epithelial cell differentiation / negative regulation of intracellular estrogen receptor signaling pathway / proximal/distal pattern formation / positive regulation of cell cycle G1/S phase transition / positive regulation of fibroblast apoptotic process / WW domain binding / cranial skeletal system development / skin morphogenesis / sympathetic nervous system development / post-anal tail morphogenesis / embryonic forelimb morphogenesis / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / embryonic hindlimb morphogenesis / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / hair follicle morphogenesis / positive regulation of Notch signaling pathway / regulation of epidermal cell division / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / epithelial cell development / TP53 Regulates Transcription of Caspase Activators and Caspases / positive regulation of stem cell proliferation / odontogenesis of dentin-containing tooth / negative regulation of cellular senescence / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / keratinocyte proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / establishment of skin barrier / Pyroptosis / positive regulation of osteoblast differentiation / keratinocyte differentiation / MDM2/MDM4 family protein binding / Notch signaling pathway / positive regulation of apoptotic signaling pathway / stem cell proliferation / skeletal system development / determination of adult lifespan / promoter-specific chromatin binding / TP53 Regulates Metabolic Genes / RNA polymerase II transcription regulatory region sequence-specific DNA binding / protein tetramerization / cellular senescence / p53 binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / transcription by RNA polymerase II / damaged DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / dendrite / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, C. / Herzberg, O. | ||||||
![]() | ![]() Title: Pliable DNA Conformation of Response Elements Bound to Transcription Factor p63. Authors: Chen, C. / Gorlatova, N. / Herzberg, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 373.6 KB | Display | ![]() |
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PDB format | ![]() | 301.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3us1C ![]() 3us2C ![]() 3qynS S: Starting model for refinement C: citing same article ( |
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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: Protein | Mass: 22683.861 Da / Num. of mol.: 4 / Fragment: DNA binding domain (UNP residues 166-362) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | Mass: 6748.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: P63 response element with AT Spacer #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 14% PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 5, 2010 / Details: mirrors |
Radiation | Monochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03320357 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→60 Å / Num. all: 47269 / Num. obs: 47258 / % possible obs: 99.99 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 3.5 / Redundancy: 12.8 % / Biso Wilson estimate: 50.4 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3.5 / Num. unique all: 3446 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3QYN Resolution: 2.5→59.802 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 28.66 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.183 Å2 / ksol: 0.283 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→59.802 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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