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Open data
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Basic information
Entry | Database: PDB / ID: 8hib | ||||||||||||||||||
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Title | The crystal structure of Pygo2-LDB1-SSBP2 triple complex | ||||||||||||||||||
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![]() | TRANSCRIPTION / Protein binding / Complex | ||||||||||||||||||
Function / homology | ![]() histone acetyltransferase regulator activity / Expression and translocation of olfactory receptors / regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / spermatid nucleus differentiation / regulation of mammary gland epithelial cell proliferation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / epithelial structure maintenance ...histone acetyltransferase regulator activity / Expression and translocation of olfactory receptors / regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / spermatid nucleus differentiation / regulation of mammary gland epithelial cell proliferation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / epithelial structure maintenance / beta-catenin-TCF complex / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / LIM domain binding / mammary gland development / gastrulation with mouth forming second / Cardiogenesis / lens development in camera-type eye / anterior/posterior axis specification / regulation of focal adhesion assembly / roof of mouth development / cell leading edge / somatic stem cell population maintenance / positive regulation of cell adhesion / hair follicle development / developmental growth / canonical Wnt signaling pathway / regulation of cell migration / kidney development / Deactivation of the beta-catenin transactivating complex / positive regulation of transcription elongation by RNA polymerase II / Formation of the beta-catenin:TCF transactivating complex / brain development / neuron differentiation / Wnt signaling pathway / Regulation of expression of SLITs and ROBOs / nervous system development / RUNX1 regulates transcription of genes involved in differentiation of HSCs / single-stranded DNA binding / histone binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / transcription coactivator activity / cell adhesion / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Wang, H.Y. / Yan, X.X. / Xu, W.Q. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The crystal structure of Pygo2-LDB1-SSBP2 triple complex Authors: Wang, H.Y. / Yan, X.X. / Xu, W.Q. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.8 KB | Display | ![]() |
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PDB format | ![]() | 145.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6tydS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 27294.443 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 10863.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein/peptide | | Mass: 2966.210 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: mutant 58Y was generated for monitoring UV280 to know where proteins are during purification Source: (gene. exp.) ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 100 mM Li2SO4, 100 mM sodium citrate tribasic dihydrate pH 5.6, 1% v/v PEG400, and 10 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→20 Å / Num. obs: 30828 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.998 / Net I/σ(I): 44.86 |
Reflection shell | Resolution: 2.45→2.52 Å / Num. unique obs: 2491 / CC1/2: 0.614 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6TYD Resolution: 2.45→19.92 Å / SU ML: 0.36 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 25.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→19.92 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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