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- PDB-3qym: Structure of p63 DNA Binding Domain in Complex with a 10 Base Pai... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qym | ||||||
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Title | Structure of p63 DNA Binding Domain in Complex with a 10 Base Pair A/T Rich Response Element Half Site | ||||||
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![]() | TRANSCRIPTION ACTIVATOR/DNA / B DNA double helix / protein-DNA complex / zinc binding / beta sandwich / greek key / transcription factor / DNA binding / 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 fibroblast apoptotic process / positive regulation of cell cycle G1/S phase transition / WW domain binding / skin morphogenesis / cranial skeletal system development / sympathetic nervous system development / post-anal tail morphogenesis / embryonic forelimb morphogenesis / 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 / positive regulation of stem cell proliferation / epithelial cell development / TP53 Regulates Transcription of Caspase Activators and Caspases / 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 / stem cell proliferation / skeletal system development / determination of adult lifespan / promoter-specific chromatin binding / positive regulation of apoptotic signaling pathway / TP53 Regulates Metabolic Genes / protein tetramerization / RNA polymerase II transcription regulatory region sequence-specific DNA binding / 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 / apoptotic process / DNA damage response / chromatin binding / dendrite / 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 / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Herzberg, O. / Chen, C. | ||||||
![]() | ![]() Title: Structures of p63 DNA binding domain in complexes with half-site and with spacer-containing full response elements. Authors: Chen, C. / Gorlatova, N. / Kelman, Z. / Herzberg, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 714 KB | Display | ![]() |
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PDB format | ![]() | 587.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 517.5 KB | Display | ![]() |
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Full document | ![]() | 637.5 KB | Display | |
Data in XML | ![]() | 72.1 KB | Display | |
Data in CIF | ![]() | 92.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qynC ![]() 2adyS C: citing same article ( 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | The biological unit is formed by a full response element, which binds two protein dimers. Protein dimer-dimer interaction is possible only if the two half sites are contiguous, and the relative orientation between the two protein dimers may vary. It is unknown which of the two arrangements of p63 dimers (BIOMOLECULE 1 and 2 versus BIOMOLECULE 3) is biologically relevant. |
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Components
#1: Protein | Mass: 22683.861 Da / Num. of mol.: 8 / Fragment: DNA binding domain (UNP residues 166-362) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | Mass: 3043.029 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: contains a consensus P63 binding motif #3: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 10% PEG3350, 0.2 M ammonium formate, 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 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9198 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→104.257 Å / Num. all: 36604 / Num. obs: 36604 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 85.29 Å2 / Rsym value: 0.14 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 3.2→3.28 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 2610 / Rsym value: 0.433 / % possible all: 94.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ADY Resolution: 3.2→19.719 Å / SU ML: 0.52 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 31.77 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.093 Å2 / ksol: 0.281 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.2→19.719 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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