+Open data
-Basic information
Entry | Database: PDB / ID: 6jk0 | ||||||
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Title | Crystal Structure of YAP1 and Dendrin complex | ||||||
Components | Transcriptional coactivator YAP1,Dendrin | ||||||
Keywords | SIGNALING PROTEIN / WW tandem / PY tandem / KIBRA / PTPN14 | ||||||
Function / homology | Function and homology information Nuclear signaling by ERBB4 / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / Signaling by Hippo / intestinal epithelial cell differentiation / enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / glandular epithelial cell differentiation ...Nuclear signaling by ERBB4 / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / Signaling by Hippo / intestinal epithelial cell differentiation / enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / bud elongation involved in lung branching / RUNX1 regulates transcription of genes involved in differentiation of HSCs / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / heart process / positive regulation of organ growth / trophectodermal cell differentiation / paraxial mesoderm development / regulation of stem cell proliferation / hippo signaling / tissue homeostasis / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / female germ cell nucleus / dendritic spine membrane / regulation of canonical Wnt signaling pathway / proline-rich region binding / negative regulation of epithelial cell differentiation / organ growth / interleukin-6-mediated signaling pathway / positive regulation of stem cell population maintenance / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / somatic stem cell population maintenance / blastocyst development / regulation of neurogenesis / signal transduction in response to DNA damage / canonical Wnt signaling pathway / vasculogenesis / positive regulation of osteoblast differentiation / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / epithelial cell proliferation / positive regulation of epithelial cell proliferation / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / wound healing / cell morphogenesis / cellular response to gamma radiation / positive regulation of protein localization to nucleus / transcription corepressor activity / cell-cell junction / positive regulation of canonical Wnt signaling pathway / regulation of cell population proliferation / positive regulation of cell growth / regulation of gene expression / protein-containing complex assembly / postsynaptic membrane / perikaryon / DNA-binding transcription factor binding / cell population proliferation / transcription regulator complex / transcription coactivator activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / chromatin binding / dendrite / positive regulation of cell population proliferation / positive regulation of gene expression / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Lin, Z. / Yang, Z. / Ji, Z. / Zhang, M. | ||||||
Citation | Journal: Elife / Year: 2019 Title: Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity. Authors: Lin, Z. / Yang, Z. / Xie, R. / Ji, Z. / Guan, K. / Zhang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jk0.cif.gz | 59.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jk0.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 6jk0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jk0_validation.pdf.gz | 431.4 KB | Display | wwPDB validaton report |
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Full document | 6jk0_full_validation.pdf.gz | 432.1 KB | Display | |
Data in XML | 6jk0_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 6jk0_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/6jk0 ftp://data.pdbj.org/pub/pdb/validation_reports/jk/6jk0 | HTTPS FTP |
-Related structure data
Related structure data | 6j68C 6jjwC 6jjxC 6jjyC 6jjzC 6jk1C 4rexS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14689.280 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: YAP1 (residues 156-247 from Uniprot P46938) linked Dendrin (residues 222-241 from Uniprot Q80TS7) Source: (gene. exp.) Mus musculus (house mouse) / Gene: Yap1, Yap, Yap65, Ddn, Gm748, Kiaa0749 / Production host: Escherichia coli (E. coli) / References: UniProt: P46938, UniProt: Q80TS7 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 7.67 Å3/Da / Density % sol: 83.96 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25-30% w/v PEG400, 200mM CaCl2, 100mM HEPS (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 8993 / % possible obs: 99.9 % / Redundancy: 34.6 % / Rmerge(I) obs: 0.225 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 3.1→3.15 Å / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2 / Num. unique obs: 444 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4REX Resolution: 3.1→32.059 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→32.059 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 9.2232 Å / Origin y: 49.3012 Å / Origin z: 68.9995 Å
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Refinement TLS group | Selection details: all |