+Open data
-Basic information
Entry | Database: PDB / ID: 7urd | |||||||||
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Title | Human PORCN in complex with LGK974 and WNT3A peptide | |||||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / inhibitor-bound / substrate-bound / complex / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information [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 / Wnt-Frizzled-LRP5/6 complex / positive regulation of cell-cell adhesion mediated by cadherin / glycoprotein metabolic process / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / synaptic vesicle recycling / Signaling by RNF43 mutants / positive regulation of cardiac muscle cell differentiation / WNT ligand biogenesis and trafficking / cell proliferation in forebrain / secondary palate development / 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 / Wnt-protein binding / dorsal/ventral neural tube patterning / negative regulation of dopaminergic neuron differentiation / midbrain dopaminergic neuron differentiation / regulation of postsynapse to nucleus signaling pathway / post-anal tail morphogenesis / mammary gland development / positive regulation of neural precursor cell proliferation / frizzled binding / positive regulation of hepatocyte proliferation / Class B/2 (Secretin family receptors) / myoblast differentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / inner ear morphogenesis / negative regulation of fat cell differentiation / regulation of synapse organization / heart looping / fat cell differentiation / B cell proliferation / Formation of paraxial mesoderm / skeletal muscle cell differentiation / regulation of postsynaptic membrane neurotransmitter receptor levels / AMPA glutamate receptor complex / positive regulation of receptor internalization / hemopoiesis / regulation of presynapse assembly / canonical Wnt signaling pathway / cell fate commitment / regulation of microtubule cytoskeleton organization / positive regulation of B cell proliferation / cellular response to retinoic acid / Regulation of FZD by ubiquitination / extracellular matrix organization / TCF dependent signaling in response to WNT / cytokine activity / axon guidance / positive regulation of cytokine production / hippocampus development / positive regulation of protein localization to plasma membrane / modulation of chemical synaptic transmission / protein localization / neuron differentiation / platelet aggregation / osteoblast differentiation / Wnt signaling pathway / negative regulation of neurogenesis / Golgi lumen / positive regulation of canonical Wnt signaling pathway / endocytic vesicle membrane / negative regulation of neuron projection development / presynapse / positive regulation of peptidyl-serine phosphorylation / heart development / early endosome membrane / cell population proliferation / in utero embryonic development / 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 / glutamatergic synapse Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å | |||||||||
Authors | Liu, Y. / Qi, X. / Li, X. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nature / Year: 2022 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7urd.cif.gz | 138.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7urd.ent.gz | 105.8 KB | Display | PDB format |
PDBx/mmJSON format | 7urd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/7urd ftp://data.pdbj.org/pub/pdb/validation_reports/ur/7urd | HTTPS FTP |
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-Related structure data
Related structure data | 26709MC 7uraC 7urcC 7ureC 7urfC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Homo sapiens (human) / Gene: PORCN, MG61, PORC, PPN / Production host: Homo sapiens (human) 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.) Homo sapiens (human) / References: UniProt: P56704 |
-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.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
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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.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
-Non-polymers , 5 types, 6 molecules
#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 |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) |
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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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / 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) |
-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 | ||||||||||||||||||||||||
Refine LS restraints |
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