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Open data
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Basic information
Entry | Database: PDB / ID: 7ura | |||||||||
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Title | Human PORCN in complex with Palmitoleoyl-CoA | |||||||||
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![]() | TRANSFERASE/TRANSFERASE INHIBITOR / CoA-bound / complex / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
Function / homology | ![]() [Wnt protein] O-palmitoleoyl transferase / LGK974 inhibits PORCN / protein palmitoleylation / palmitoleoyltransferase activity / Wnt protein secretion / lipid modification / protein lipidation / WNT ligand biogenesis and trafficking / glycoprotein metabolic process / Wnt-protein binding ...[Wnt protein] O-palmitoleoyl transferase / LGK974 inhibits PORCN / protein palmitoleylation / palmitoleoyltransferase activity / Wnt protein secretion / lipid modification / protein lipidation / WNT ligand biogenesis and trafficking / glycoprotein metabolic process / Wnt-protein binding / regulation of postsynaptic membrane neurotransmitter receptor levels / AMPA glutamate receptor complex / Wnt signaling pathway / glutamatergic synapse / endoplasmic reticulum membrane / endoplasmic reticulum / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 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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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.2 KB | Display | ![]() |
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PDB format | ![]() | 103.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 26707MC ![]() 7urcC ![]() 7urdC ![]() 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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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 1 types, 1 molecules A
#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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-Antibody , 2 types, 2 molecules LH
#2: Antibody | Mass: 25673.693 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#3: 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/OH6.gif)
![](data/chem/img/ZN.gif)
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![](data/chem/img/AJP.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CLR.gif)
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#4: Chemical | ChemComp-OH6 / ~{ | ||||
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#5: Chemical | ChemComp-ZN / | ||||
#6: Chemical | #7: Chemical | ChemComp-AJP / | #8: Chemical | ChemComp-OLA / | |
-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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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 |
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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: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 233902 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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