8CTG | pdb_00008ctg

Deposited: 2022-05-14 Released: 2023-03-15
Deposition Author(s): Tsutsumi, N., Jude, K.M., Garcia, K.C.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Howard Hughes Medical Institute (HHMI), Ludwig Institute for Cancer Research (LICR)

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

(2023) Proc Natl Acad Sci U S A 120: e2218238120-e2218238120

PubMed Abstract:
Wnt morphogens are critical for embryonic development and tissue regeneration. Canonical Wnts form ternary receptor complexes composed of tissue-specific Frizzled (Fzd) receptors together with the shared LRP5/6 coreceptors to initiate β-catenin signaling. The cryo-EM structure of a ternary initiation complex of an affinity-matured XWnt8-Frizzled8-LRP6 complex elucidates the basis of coreceptor discrimination by canonical Wnts by means of their N termini and linker domains that engage the LRP6 E1E2 domain funnels. Chimeric Wnts bearing modular linker "grafts" were able to transfer LRP6 domain specificity between different Wnts and enable non-canonical Wnt5a to signal through the canonical pathway. Synthetic peptides comprising the linker domain serve as Wnt-specific antagonists. The structure of the ternary complex provides a topological blueprint for the orientation and proximity of Frizzled and LRP6 within the Wnt cell surface signalosome.

Organizational Affiliation

Macromolecule Content

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Frizzled-8	A	132	Mus musculus	Mutation(s): 0 Gene Names: Fzd8
UniProt & NIH Common Fund Data Resources
Find proteins for Q61091 (Mus musculus) Explore Q61091 Go to UniProtKB: Q61091
IMPC: MGI:108460
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q61091
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Wnt-8	B	327	Xenopus laevis	Mutation(s): 0 Gene Names: wnt8
UniProt
Find proteins for P28026 (Xenopus laevis) Explore P28026 Go to UniProtKB: P28026
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28026
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Low-density lipoprotein receptor-related protein 6	C	649	Homo sapiens	Mutation(s): 0 Gene Names: LRP6
UniProt & NIH Common Fund Data Resources
Find proteins for O75581 (Homo sapiens) Explore O75581 Go to UniProtKB: O75581
PHAROS: O75581 GTEx: ENSG00000070018
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75581
Sequence Annotations Expand
Reference Sequence

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PAM Query on PAM Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	PALMITOLEIC ACID C₁₆ H₃₀ O₂ SECPZKHBENQXJG-FPLPWBNLSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.3

& Funding Information

Deposition Author(s):

Tsutsumi, N.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R37AI051321
Howard Hughes Medical Institute (HHMI)	United States	--
Ludwig Institute for Cancer Research (LICR)	United States	--