7URF

Human HHAT H379C in complex with SHH N-terminal peptide


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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 Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. xiaochun.li@utsouthwestern.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-cysteine N-palmitoyltransferase HHAT500Homo sapiensMutation(s): 0 
Gene Names: HHATMART2SKI1
EC: 2.3.1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VTY9 (Homo sapiens)
Explore Q5VTY9 
Go to UniProtKB:  Q5VTY9
PHAROS:  Q5VTY9
GTEx:  ENSG00000054392 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5VTY9
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SHH-N peptide7Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15465 (Homo sapiens)
Explore Q15465 
Go to UniProtKB:  Q15465
PHAROS:  Q15465
GTEx:  ENSG00000164690 
Entity Groups  
UniProt GroupQ15465
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
3H02 heavy chainC [auth O]250Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
3H02 light chainD [auth P]239Mus musculusMutation(s): 0 
Entity Groups  
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AJP
Query on AJP

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
Digitonin
C56 H92 O29
UVYVLBIGDKGWPX-KUAJCENISA-N
PKZ
Query on PKZ

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
Palmitoyl-CoA
C37 H66 N7 O17 P3 S
MNBKLUUYKPBKDU-BBECNAHFSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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