7URD

Human PORCN in complex with LGK974 and WNT3A peptide


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanisms and inhibition of Porcupine-mediated Wnt acylation.

Liu, Y.Qi, X.Donnelly, L.Elghobashi-Meinhardt, N.Long, T.Zhou, R.W.Sun, Y.Wang, B.Li, X.

(2022) Nature 607: 816-822

  • DOI: https://doi.org/10.1038/s41586-022-04952-2
  • Primary Citation of Related Structures:  
    7URA, 7URC, 7URD, 7URE, 7URF

  • PubMed Abstract: 

    Wnt signalling is essential for regulation of embryonic development and adult tissue homeostasis 1-3 , and aberrant Wnt signalling is frequently associated with cancers 4 . Wnt signalling requires palmitoleoylation on a hairpin 2 motif by the endoplasmic reticulum-resident membrane-bound O-acyltransferase Porcupine 5-7 (PORCN). This modification is indispensable for Wnt binding to its receptor Frizzled, which triggers signalling 8,9 . 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 10 ; 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.


  • Organizational Affiliation

    Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Protein-serine O-palmitoleoyltransferase porcupine464Homo sapiensMutation(s): 0 
Gene Names: PORCNMG61PORCPPN
EC: 2.3.1.250
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H237 (Homo sapiens)
Explore Q9H237 
Go to UniProtKB:  Q9H237
PHAROS:  Q9H237
GTEx:  ENSG00000102312 
Entity Groups  
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UniProt GroupQ9H237
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Protein Wnt-3a peptide22Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P56704 (Homo sapiens)
Explore P56704 
Go to UniProtKB:  P56704
PHAROS:  P56704
GTEx:  ENSG00000154342 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56704
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
2C11 light chainC [auth L]234Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
2C11 heavy chainD [auth H]250Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AJP
Query on AJP

Download Ideal Coordinates CCD File 
H [auth A]Digitonin
C56 H92 O29
UVYVLBIGDKGWPX-KUAJCENISA-N
O50 (Subject of Investigation/LOI)
Query on O50

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E [auth A]2-[(2P)-2',3-dimethyl[2,4'-bipyridin]-5-yl]-N-[(5P)-5-(pyrazin-2-yl)pyridin-2-yl]acetamide
C23 H20 N6 O
XXYGTCZJJLTAGH-UHFFFAOYSA-N
CLR
Query on CLR

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F [auth A],
G [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
OLA
Query on OLA

Download Ideal Coordinates CCD File 
I [auth A]OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
J [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
O50 BindingDB:  7URD IC50: min: 0.38, max: 0.9 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--
Welch FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Database references
  • Version 1.2: 2022-08-10
    Changes: Database references