+Open data
-Basic information
Entry | Database: PDB / ID: 7z71 | ||||||
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Title | Crystal structure of p63 DBD in complex with darpin C14 | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / p63 / TP63 / darpin / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information 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 / Notch signaling pathway / MDM2/MDM4 family protein binding / stem cell proliferation / skeletal system development / determination of adult lifespan / promoter-specific chromatin binding / TP53 Regulates Metabolic Genes / positive regulation of apoptotic signaling pathway / 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 | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Chaikuad, A. / Strubel, A. / Doetsch, V. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Funding support | 1items
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Citation | Journal: Cell Death Differ. / Year: 2022 Title: Designed Ankyrin Repeat Proteins as a tool box for analyzing p63. Authors: Strubel, A. / Munick, P. / Chaikuad, A. / Dreier, B. / Schaefer, J. / Gebel, J. / Osterburg, C. / Tuppi, M. / Schafer, B. / Knapp, S. / Pluckthun, A. / Dotsch, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z71.cif.gz | 288 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z71.ent.gz | 232.9 KB | Display | PDB format |
PDBx/mmJSON format | 7z71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z71_validation.pdf.gz | 436.8 KB | Display | wwPDB validaton report |
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Full document | 7z71_full_validation.pdf.gz | 440.2 KB | Display | |
Data in XML | 7z71_validation.xml.gz | 33 KB | Display | |
Data in CIF | 7z71_validation.cif.gz | 50 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/7z71 ftp://data.pdbj.org/pub/pdb/validation_reports/z7/7z71 | HTTPS FTP |
-Related structure data
Related structure data | 7z72C 7z73C 7z7eC 3qynS 6fpbS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 22752.920 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TP63, KET, P63, P73H, P73L, TP73L / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H3D4 #2: Protein | Mass: 16632.615 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.52 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% PEG 3350, 0.2 M sodium chloride, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 3, 2020 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.85→44.64 Å / Num. obs: 58153 / % possible obs: 91.6 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.025 / Rrim(I) all: 0.048 / Net I/σ(I): 22 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3qyn, 6fpb Resolution: 1.85→42.69 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.005 / SU ML: 0.066 / SU R Cruickshank DPI: 0.1219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.01 Å2 / Biso mean: 27.074 Å2 / Biso min: 14.71 Å2
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Refinement step | Cycle: final / Resolution: 1.85→42.69 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / 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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