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- PDB-8x3s: Crystal structure of human WDR5 in complex with PTEN -

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Basic information

Entry
Database: PDB / ID: 8x3s
TitleCrystal structure of human WDR5 in complex with PTEN
Components
  • Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
  • WD repeat-containing protein 5
KeywordsCELL CYCLE / Complex / Cell Proliferation / Cancer
Function / homology
Function and homology information


PTEN Loss of Function in Cancer / inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity / central nervous system myelin maintenance ...PTEN Loss of Function in Cancer / inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / 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 / presynaptic membrane assembly / Regulation of PTEN mRNA translation / synapse maturation / Negative regulation of the PI3K/AKT network / negative regulation of cell cycle G1/S phase transition / cellular response to electrical stimulus / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of axonogenesis / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / Transcriptional Regulation by MECP2 / myelin sheath adaxonal region / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of organ growth / forebrain morphogenesis / negative regulation of excitatory postsynaptic potential / negative regulation of focal adhesion assembly / phosphatidylinositol dephosphorylation / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / anaphase-promoting complex binding / Schmidt-Lanterman incisure / dentate gyrus development / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / ubiquitin ligase activator activity / positive regulation of ubiquitin protein ligase activity / phosphatidylinositol biosynthetic process / dendritic spine morphogenesis / MLL3/4 complex / negative regulation of cell size / maternal behavior / spindle assembly involved in female meiosis / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / negative regulation of peptidyl-serine phosphorylation / NSL complex / positive regulation of ubiquitin-dependent protein catabolic process / histone H3K4 methyltransferase activity / Cardiogenesis / negative regulation of epithelial to mesenchymal transition / molecular function inhibitor activity / protein serine/threonine phosphatase activity / histone methyltransferase complex / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / negative regulation of G1/S transition of mitotic cell cycle / Formation of WDR5-containing histone-modifying complexes / regulation of neuron projection development / ubiquitin-specific protease binding / Synthesis of IP3 and IP4 in the cytosol / social behavior / locomotor rhythm / adult behavior / negative regulation of vascular associated smooth muscle cell proliferation / Synthesis of PIPs at the plasma membrane / positive regulation of intracellular signal transduction / regulation of cell division / regulation of embryonic development / phosphoprotein phosphatase activity / MLL1 complex / negative regulation of cellular senescence / histone acetyltransferase complex / positive regulation of excitatory postsynaptic potential / negative regulation of osteoblast differentiation / prepulse inhibition / multicellular organismal response to stress / synapse assembly / protein dephosphorylation / : / protein tyrosine phosphatase activity / positive regulation of gluconeogenesis / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / transcription initiation-coupled chromatin remodeling / Regulation of PTEN localization
Similarity search - Function
Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / PTEN, phosphatase domain / : / Inositol hexakisphosphate / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein ...Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / PTEN, phosphatase domain / : / Inositol hexakisphosphate / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Polymorphic toxin system, DSP-PTPase phosphatase / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / C2 domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsLiu, Y. / Huang, X. / Shang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271309 China
CitationJournal: Cell Death Dis / Year: 2024
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
DepositionNov 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: WD repeat-containing protein 5
B: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN


Theoretical massNumber of molelcules
Total (without water)37,9452
Polymers37,9452
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-3 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.460, 63.750, 92.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein WD repeat-containing protein 5


Mass: 34478.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5 / Production host: Escherichia coli (E. coli) / References: UniProt: P61964
#2: Protein/peptide Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN / Mutated in multiple advanced cancers 1 / Phosphatase and tensin homolog


Mass: 3466.780 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTEN, MMAC1, TEP1 / Production host: Escherichia coli (E. coli)
References: UniProt: P60484, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase, phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 32.11 %
Description: The entry contains friedel pairs in I_plus/minus columns
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.87→1.91 Å / Num. unique obs: 1831 / CC1/2: 0.627

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→29.19 Å / Cross valid method: FREE R-VALUE
Details: The entry contains friedel pairs in I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2586 --
Rwork0.224 --
obs-22670 97 %
Refinement stepCycle: LAST / Resolution: 1.87→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2429 0 0 125 2554

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