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Open data
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Basic information
Entry | Database: PDB / ID: 7urd | |||||||||
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Title | Human PORCN in complex with LGK974 and WNT3A peptide | |||||||||
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![]() | TRANSFERASE/TRANSFERASE INHIBITOR / inhibitor-bound / substrate-bound / complex / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
Function / homology | ![]() [Wnt protein] O-palmitoleoyl transferase / Wnt signaling pathway involved in forebrain neuroblast division / positive regulation of dermatome development / axis elongation involved in somitogenesis / calcium ion transmembrane transport via low voltage-gated calcium channel / : / LGK974 inhibits PORCN / protein palmitoleylation / positive regulation of collateral sprouting in absence of injury / palmitoleoyltransferase activity ...[Wnt protein] O-palmitoleoyl transferase / Wnt signaling pathway involved in forebrain neuroblast division / positive regulation of dermatome development / axis elongation involved in somitogenesis / calcium ion transmembrane transport via low voltage-gated calcium channel / : / LGK974 inhibits PORCN / protein palmitoleylation / positive regulation of collateral sprouting in absence of injury / palmitoleoyltransferase activity / positive regulation of mesodermal cell fate specification / paraxial mesodermal cell fate commitment / cell proliferation in midbrain / spinal cord association neuron differentiation / Formation of the posterior neural plate / Wnt protein secretion / lipid modification / COP9 signalosome assembly / protein lipidation / positive regulation of cell-cell adhesion mediated by cadherin / Wnt-Frizzled-LRP5/6 complex / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / synaptic vesicle recycling / Signaling by RNF43 mutants / WNT ligand biogenesis and trafficking / glycoprotein metabolic process / positive regulation of cardiac muscle cell differentiation / cell proliferation in forebrain / secondary palate development / Specification of the neural plate border / negative regulation of axon extension involved in axon guidance / somatic stem cell division / non-canonical Wnt signaling pathway / co-receptor binding / cardiac muscle cell fate commitment / presynapse assembly / positive regulation of skeletal muscle tissue development / dorsal/ventral neural tube patterning / negative regulation of dopaminergic neuron differentiation / midbrain dopaminergic neuron differentiation / Wnt-protein binding / regulation of postsynapse to nucleus signaling pathway / mammary gland development / post-anal tail morphogenesis / positive regulation of neural precursor cell proliferation / frizzled binding / positive regulation of hepatocyte proliferation / Class B/2 (Secretin family receptors) / Disassembly of the destruction complex and recruitment of AXIN to the membrane / myoblast differentiation / inner ear morphogenesis / regulation of synapse organization / negative regulation of fat cell differentiation / B cell proliferation / fat cell differentiation / heart looping / Formation of paraxial mesoderm / regulation of postsynaptic membrane neurotransmitter receptor levels / skeletal muscle cell differentiation / positive regulation of receptor internalization / AMPA glutamate receptor complex / hemopoiesis / regulation of presynapse assembly / canonical Wnt signaling pathway / cell fate commitment / regulation of microtubule cytoskeleton organization / cellular response to retinoic acid / positive regulation of B cell proliferation / Regulation of FZD by ubiquitination / extracellular matrix organization / TCF dependent signaling in response to WNT / positive regulation of cytokine production / cytokine activity / hippocampus development / positive regulation of protein localization to plasma membrane / axon guidance / modulation of chemical synaptic transmission / neuron differentiation / protein localization / Wnt signaling pathway / platelet aggregation / negative regulation of neurogenesis / Golgi lumen / osteoblast differentiation / endocytic vesicle membrane / positive regulation of canonical Wnt signaling pathway / presynapse / positive regulation of peptidyl-serine phosphorylation / negative regulation of neuron projection development / heart development / early endosome membrane / in utero embryonic development / cell population proliferation / transcription by RNA polymerase II / transcription coactivator activity / receptor ligand activity / positive regulation of protein phosphorylation / protein domain specific binding / endoplasmic reticulum lumen / signaling receptor binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å | |||||||||
![]() | Liu, Y. / Qi, X. / Li, X. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanisms and inhibition of Porcupine-mediated Wnt acylation. Authors: Yang Liu / Xiaofeng Qi / Linda Donnelly / Nadia Elghobashi-Meinhardt / Tao Long / Rich W Zhou / Yingyuan Sun / Boyuan Wang / Xiaochun Li / ![]() ![]() Abstract: Wnt signalling is essential for regulation of embryonic development and adult tissue homeostasis, and aberrant Wnt signalling is frequently associated with cancers. Wnt signalling requires ...Wnt signalling is essential for regulation of embryonic development and adult tissue homeostasis, and aberrant Wnt signalling is frequently associated with cancers. Wnt signalling requires palmitoleoylation on a hairpin 2 motif by the endoplasmic reticulum-resident membrane-bound O-acyltransferase Porcupine (PORCN). This modification is indispensable for Wnt binding to its receptor Frizzled, which triggers signalling. Here we report four cryo-electron microscopy structures of human PORCN: the complex with the palmitoleoyl-coenzyme A (palmitoleoyl-CoA) substrate; the complex with the PORCN inhibitor LGK974, an anti-cancer drug currently in clinical trials; the complex with LGK974 and WNT3A hairpin 2 (WNT3Ap); and the complex with a synthetic palmitoleoylated WNT3Ap analogue. The structures reveal that hairpin 2 of WNT3A, which is well conserved in all Wnt ligands, inserts into PORCN from the lumenal side, and the palmitoleoyl-CoA accesses the enzyme from the cytosolic side. The catalytic histidine triggers the transfer of the unsaturated palmitoleoyl group to the target serine on the Wnt hairpin 2, facilitated by the proximity of the two substrates. The inhibitor-bound structure shows that LGK974 occupies the palmitoleoyl-CoA binding site to prevent the reaction. Thus, this work provides a mechanism for Wnt acylation and advances the development of PORCN inhibitors for cancer treatment. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 138.5 KB | Display | ![]() |
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PDB format | ![]() | 105.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 35.4 KB | Display | |
Data in CIF | ![]() | 49.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 26709MC ![]() 7uraC ![]() 7urcC ![]() 7ureC ![]() 7urfC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Isoform 2 of ... , 2 types, 2 molecules AB
#1: Protein | Mass: 52824.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q9H237, [Wnt protein] O-palmitoleoyl transferase |
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#2: Protein/peptide | Mass: 2529.036 Da / Num. of mol.: 1 / Fragment: residues 199-220 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Antibody , 2 types, 2 molecules LH
#3: Antibody | Mass: 25673.693 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#4: Antibody | Mass: 26933.135 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 5 types, 6 molecules ![](data/chem/img/O50.gif)
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#5: Chemical | ChemComp-O50 / | ||||||
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#6: Chemical | #7: Chemical | ChemComp-AJP / | #8: Chemical | ChemComp-OLA / | #9: Chemical | ChemComp-ZN / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 8.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 397217 / Symmetry type: POINT | ||||||||||||||||||||||||
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