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Open data
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Basic information
Entry | Database: PDB / ID: 6jk1 | ||||||
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Title | Crystal Structure of YAP1 and Dendrin complex 2 | ||||||
![]() | Dendrin,Transcriptional coactivator YAP1 | ||||||
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Function / homology | ![]() 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 / hippo signaling / regulation of stem cell proliferation / 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 / positive regulation of stem cell population maintenance / interleukin-6-mediated signaling pathway / negative regulation of fat cell differentiation / positive regulation of Notch signaling pathway / somatic stem cell population maintenance / blastocyst development / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, Z. / Yang, Z. / Ji, Z. / Zhang, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.5 KB | Display | ![]() |
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PDB format | ![]() | 72.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6j68C ![]() 6jjwC ![]() 6jjxC ![]() 6jjyC ![]() 6jjzC ![]() 6jk0SC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12768.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Dendrin (residues 222-241 from Uniprot Q80TS7) linked YAP1 (residues 156-247 from Uniprot P46938) Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.06 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 28-35% w/v pentaerythritol propoxylat 426 (5/4 PO/OH), 100mM HEPES (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→50 Å / Num. obs: 24702 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 32.8 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1210 / % possible all: 100 |
Serial crystallography sample delivery | Method: fixed target |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6JK0 Resolution: 2→29.191 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.21
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.191 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: 47.8898 Å / Origin y: 63.1532 Å / Origin z: 41.9106 Å
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Refinement TLS group | Selection details: all |