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Open data
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Basic information
Entry | Database: PDB / ID: 8x3s | ||||||
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Title | Crystal structure of human WDR5 in complex with PTEN | ||||||
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![]() | CELL CYCLE / Complex / Cell Proliferation / Cancer | ||||||
Function / homology | ![]() inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / PTEN Loss of Function in Cancer / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / regulation of cellular component size / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity ...inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / PTEN Loss of Function in Cancer / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / regulation of cellular component size / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity / central nervous system myelin maintenance / negative regulation of wound healing, spreading of epidermal cells / phosphatidylinositol-3-phosphate phosphatase activity / central nervous system neuron axonogenesis / postsynaptic density assembly / neuron-neuron synaptic transmission / negative regulation of dendritic spine morphogenesis / Regulation of PTEN mRNA translation / synapse maturation / presynaptic membrane assembly / Negative regulation of the PI3K/AKT network / cellular response to electrical stimulus / negative regulation of cell cycle G1/S phase transition / negative regulation of axonogenesis / Transcriptional Regulation by MECP2 / myelin sheath adaxonal region / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / negative regulation of excitatory postsynaptic potential / negative regulation of organ growth / forebrain morphogenesis / negative regulation of focal adhesion assembly / Schmidt-Lanterman incisure / anaphase-promoting complex binding / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphatidylinositol dephosphorylation / dentate gyrus development / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of ubiquitin protein ligase activity / spindle assembly involved in female meiosis / positive regulation of ubiquitin-dependent protein catabolic process / negative regulation of cell size / phosphatidylinositol biosynthetic process / MLL3/4 complex / dendritic spine morphogenesis / Set1C/COMPASS complex / MLL1/2 complex / negative regulation of epithelial to mesenchymal transition / brain morphogenesis / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / regulation of neuron projection development / histone methyltransferase complex / regulation of tubulin deacetylation / myosin phosphatase activity / negative regulation of G1/S transition of mitotic cell cycle / protein serine/threonine phosphatase activity / molecular function inhibitor activity / protein-serine/threonine phosphatase / ubiquitin-specific protease binding / Formation of WDR5-containing histone-modifying complexes / Synthesis of IP3 and IP4 in the cytosol / regulation of cell division / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of peptidyl-serine phosphorylation / locomotor rhythm / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of cellular senescence / Synthesis of PIPs at the plasma membrane / positive regulation of excitatory postsynaptic potential / phosphoprotein phosphatase activity / social behavior / regulation of embryonic development / MLL1 complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase complex / localization / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / canonical Wnt signaling pathway / prepulse inhibition / multicellular organismal response to stress / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / synapse assembly / methylated histone binding / Regulation of PTEN localization / protein dephosphorylation / negative regulation of cell migration / protein-tyrosine-phosphatase / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of protein phosphorylation / protein tyrosine phosphatase activity / skeletal system development / locomotory behavior / central nervous system development / cell projection / gluconeogenesis / PDZ domain binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, Y. / Huang, X. / Shang, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The NTE domain of PTEN alpha / beta promotes cancer progression by interacting with WDR5 via its SSSRRSS motif. Authors: Huang, X. / Zhang, C. / Shang, X. / Chen, Y. / Xiao, Q. / Wei, Z. / Wang, G. / Zhen, X. / Xu, G. / Min, J. / Shen, S. / Liu, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.7 KB | Display | ![]() |
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PDB format | ![]() | 55 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.8 KB | Display | ![]() |
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Full document | ![]() | 436.5 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8x3rC C: citing same article ( |
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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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Unit cell |
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Components
#1: Protein | Mass: 34478.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 3466.780 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P60484, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase, phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.11 % Description: The entry contains friedel pairs in I_plus/minus columns |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M lithium sulfate monohydrate, 0.1 M HEPES at pH 7.5, 25% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 4, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→29.19 Å / Num. obs: 22670 / % possible obs: 97 % / Redundancy: 1.8 % / CC1/2: 0.994 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.87→1.91 Å / Num. unique obs: 1831 / CC1/2: 0.627 |
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Processing
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Refinement | Method to determine structure: ![]() Details: The entry contains friedel pairs in I_plus/minus columns
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Refinement step | Cycle: LAST / Resolution: 1.87→29.19 Å
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