21KR | pdb_000021kr

A Wnt3a/Fzd8-CRD/LRP6-E3E4 complex with FKBP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 21KR

This is version 1.0 of the entry. See complete history

Literature

Structural basis of Wnt signalosome extracellular complex assembly.

Yue, D.Sun, G.Cao, Y.Li, H.Yang, Y.Pan, Z.Xue, L.Zhang, L.Wang, Z.Xu, W.

(2026) Cell 

  • DOI: https://doi.org/10.1016/j.cell.2026.05.006
  • Primary Citation Related Structures: 
    21KR, 21KS, 21KT

  • PubMed Abstract: 

    Recognition of Wnt proteins by Frizzled (Fzd) receptors and the low-density lipoprotein receptor-related protein 5/6 (LRP5/6) co-receptor is essential for canonical Wnt signaling. It remains enigmatic how Wnt simultaneously interacts with Fzd and LRP5/6 and activates intracellular Wnt/β-catenin signaling. Here, we report cryo-electron microscopy (cryo-EM) structures of Wnt3a/Fzd8/LRP6 extracellular complexes captured in a 2:4:2 stoichiometry, consisting of a Wnt3a-Wnt3a homodimer, whereby each Wnt3a monomer binds to two Fzd8 receptors and one LRP6 co-receptor. This implies that Wnt3a induces Fzd cystine-rich domain (Fzd-CRD) tetramerization, which in turn could promote recruitment of oligomeric Disheveled (Dvl) to Fzd on the cytoplasmic side. Indeed, mutations of key Wnt3a-Wnt3a interface residues abolish Fzd-LRP clustering and downstream signaling, supporting a critical role of Wnt3a-Wnt3a dimerization in Wnt signalosome assembly and signaling. Our structures also show how the Wnt3a N-helical domain recognizes the LRP6 extracellular domain (LRP6-ECD) E3 β-propeller, while the Wnt3a N-C hairpin interacts with the valley between LRP6-E3 and -E4 propellers, underpinning the development of targeted Wnt therapeutics.


  • Organizational Affiliation
    • School of Life Science and Technology, ShanghaiTech University, Shanghai, China.

Macromolecule Content 

  • Total Structure Weight: 398.08 kDa 
  • Atom Count: 19,900 
  • Modeled Residue Count: 2,483 
  • Deposited Residue Count: 3,527 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein Wnt-3a
A, E
334Mus musculusMutation(s): 0 
Gene Names: Wnt3aWnt-3a
UniProt & NIH Common Fund Data Resources
Find proteins for P27467 (Mus musculus)
Explore P27467 
Go to UniProtKB:  P27467
IMPC:  MGI:98956
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27467
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P27467-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Low-density lipoprotein receptor-related protein 6,Serine/threonine-protein kinase mTOR
B, F
752Homo sapiensMutation(s): 1 
Gene Names: LRP6MTOR
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O75581 (Homo sapiens)
Explore O75581 
Go to UniProtKB:  O75581
PHAROS:  O75581
GTEx:  ENSG00000070018 
Find proteins for A0A8V8TRG9 (Homo sapiens)
Explore A0A8V8TRG9 
Go to UniProtKB:  A0A8V8TRG9
GTEx:  ENSG00000198793 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsO75581A0A8V8TRG9
Glycosylation
Glycosylation Sites: 3Go to GlyGen: O75581-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Frizzled-8,Peptidyl-prolyl cis-trans isomerase FKBP1A
C, D, G, H, I
271Homo sapiensMutation(s): 1 
Gene Names: FZD8FKBP1AFKBP1FKBP12
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H461 (Homo sapiens)
Explore Q9H461 
Go to UniProtKB:  Q9H461
PHAROS:  Q9H461
GTEx:  ENSG00000177283 
Find proteins for P62942 (Homo sapiens)
Explore P62942 
Go to UniProtKB:  P62942
PHAROS:  P62942
GTEx:  ENSG00000088832 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP62942Q9H461
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J, K, L
2N-Glycosylation

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--
National Natural Science Foundation of China (NSFC)China--
Ministry of Science and Technology (MoST, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-03
    Type: Initial release