[English] 日本語
Yorodumi
- PDB-7urd: Human PORCN in complex with LGK974 and WNT3A peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7urd
TitleHuman PORCN in complex with LGK974 and WNT3A peptide
Components
  • (Isoform 2 of ...) x 2
  • 2C11 heavy chain
  • 2C11 light chain
KeywordsTRANSFERASE/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 / protein palmitoleylation / positive regulation of dermatome development / calcium ion transmembrane transport via low voltage-gated calcium channel / palmitoleoyltransferase activity / LGK974 inhibits PORCN / protein lipidation / positive regulation of collateral sprouting in absence of injury / positive regulation of mesodermal cell fate specification ...[Wnt protein] O-palmitoleoyl transferase / Wnt signaling pathway involved in forebrain neuroblast division / protein palmitoleylation / positive regulation of dermatome development / calcium ion transmembrane transport via low voltage-gated calcium channel / palmitoleoyltransferase activity / LGK974 inhibits PORCN / protein lipidation / positive regulation of collateral sprouting in absence of injury / positive regulation of mesodermal cell fate specification / paraxial mesodermal cell fate commitment / axis elongation involved in somitogenesis / cell proliferation in midbrain / spinal cord association neuron differentiation / Wnt protein secretion / positive regulation of type B pancreatic cell proliferation / Formation of the posterior neural plate / lipid modification / COP9 signalosome assembly / Wnt-Frizzled-LRP5/6 complex / glycoprotein metabolic process / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / positive regulation of cell-cell adhesion mediated by cadherin / WNT ligand biogenesis and trafficking / Signaling by RNF43 mutants / negative regulation of axon extension involved in axon guidance / synaptic vesicle recycling / cell proliferation in forebrain / positive regulation of cardiac muscle cell differentiation / Specification of the neural plate border / secondary palate development / somatic stem cell division / cardiac muscle cell fate commitment / non-canonical Wnt signaling pathway / co-receptor binding / presynapse assembly / positive regulation of skeletal muscle tissue development / negative regulation of dopaminergic neuron differentiation / Wnt-protein binding / midbrain dopaminergic neuron differentiation / dorsal/ventral neural tube patterning / regulation of postsynapse to nucleus signaling pathway / post-anal tail morphogenesis / mammary gland development / frizzled binding / positive regulation of neural precursor cell proliferation / positive regulation of hepatocyte proliferation / myoblast differentiation / Class B/2 (Secretin family receptors) / 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 / Formation of paraxial mesoderm / fat cell differentiation / heart looping / skeletal muscle cell differentiation / hemopoiesis / AMPA glutamate receptor complex / B cell proliferation / positive regulation of receptor internalization / regulation of presynapse assembly / cell fate commitment / regulation of postsynaptic membrane neurotransmitter receptor levels / canonical Wnt signaling pathway / cellular response to retinoic acid / positive regulation of B cell proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / extracellular matrix organization / Regulation of FZD by ubiquitination / regulation of microtubule cytoskeleton organization / axon guidance / hippocampus development / positive regulation of cytokine production / cytokine activity / positive regulation of peptidyl-serine phosphorylation / TCF dependent signaling in response to WNT / positive regulation of protein localization to plasma membrane / modulation of chemical synaptic transmission / neuron differentiation / Wnt signaling pathway / negative regulation of neurogenesis / Golgi lumen / platelet aggregation / osteoblast differentiation / endocytic vesicle membrane / positive regulation of canonical Wnt signaling pathway / protein localization / presynapse / negative regulation of neuron projection development / heart development / early endosome membrane / in utero embryonic development / transcription by RNA polymerase II / positive regulation of protein phosphorylation / transcription coactivator activity / cell population proliferation / receptor ligand activity / protein domain specific binding / endoplasmic reticulum lumen
Similarity search - Function
Wnt-3 protein / : / Wnt protein, conserved site / Wnt-1 family signature. / Wnt / Wnt, C-terminal domain / wnt family / found in Wnt-1 / Membrane bound O-acyl transferase, MBOAT / MBOAT, membrane-bound O-acyltransferase family
Similarity search - Domain/homology
CHOLESTEROL / Chem-O50 / OLEIC ACID / Protein Wnt-3a / Protein-serine O-palmitoleoyltransferase porcupine
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsLiu, Y. / Qi, X. / Li, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Welch Foundation United States
CitationJournal: 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
DepositionApr 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isoform 2 of Protein-serine O-palmitoleoyltransferase porcupine
B: Isoform 2 of Protein Wnt-3a peptide
L: 2C11 light chain
H: 2C11 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,70710
Polymers107,9614
Non-polymers2,7476
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Isoform 2 of ... , 2 types, 2 molecules AB

#1: Protein Isoform 2 of Protein-serine O-palmitoleoyltransferase porcupine / Protein MG61


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
#2: Protein/peptide Isoform 2 of Protein Wnt-3a 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 2C11 light chain


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)
#4: Antibody 2C11 heavy chain


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 / 2-[(2P)-2',3-dimethyl[2,4'-bipyridin]-5-yl]-N-[(5P)-5-(pyrazin-2-yl)pyridin-2-yl]acetamide


Mass: 396.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H20N6O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#7: Chemical ChemComp-AJP / Digitonin


Mass: 1229.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C56H92O29 / Comment: detergent*YM
#8: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1LGK974 and WNT3a peptide-bound human PORCNCOMPLEX#1-#40RECOMBINANT
2Isoform 2 of Protein-serine O-palmitoleoyltransferase porcupine (E.C.2.3.1.250)COMPLEX#11RECOMBINANT
3Isoform 2 of Protein Wnt-3a peptideCOMPLEX#21SYNTHETIC
42C11 light chain, 2C11 heavy chainCOMPLEX#3-#41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
24Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
24Homo sapiens (human)9606
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 8.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 397217 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0045727
ELECTRON MICROSCOPYf_angle_d0.8347805
ELECTRON MICROSCOPYf_dihedral_angle_d6.13186
ELECTRON MICROSCOPYf_chiral_restr0.087883
ELECTRON MICROSCOPYf_plane_restr0.004924

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more