6WW2

Structure of human Frizzled5 by fiducial-assisted cryo-EM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structure of human Frizzled5 by fiducial-assisted cryo-EM supports a heterodimeric mechanism of canonical Wnt signaling.

Tsutsumi, N.Mukherjee, S.Waghray, D.Janda, C.Y.Jude, K.M.Miao, Y.Burg, J.S.Aduri, N.G.Kossiakoff, A.A.Gati, C.Garcia, K.C.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.58464
  • Primary Citation of Related Structures:  
    6WW2

  • PubMed Abstract: 

    Frizzleds (Fzd) are the primary receptors for Wnt morphogens, which are essential regulators of stem cell biology, yet the structural basis of Wnt signaling through Fzd remains poorly understood. Here we report the structure of an unliganded human Fzd5 determined by single-particle cryo-EM at 3.7 Å resolution, with the aid of an antibody chaperone acting as a fiducial marker. We also analyzed the topology of low-resolution XWnt8/Fzd5 complex particles, which revealed extreme flexibility between the Wnt/Fzd-CRD and the Fzd-TM regions. Analysis of Wnt/β-catenin signaling in response to Wnt3a versus a 'surrogate agonist' that cross-links Fzd to LRP6, revealed identical structure-activity relationships. Thus, canonical Wnt/β-catenin signaling appears to be principally reliant on ligand-induced Fzd/LRP6 heterodimerization, versus the allosteric mechanisms seen in structurally analogous class A G protein-coupled receptors, and Smoothened. These findings deepen our mechanistic understanding of Wnt signal transduction, and have implications for harnessing Wnt agonism in regenerative medicine.


  • Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
anti-BRIL Fab Heavy chainA [auth H]229Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
anti-Fab NanobodyB [auth K]123synthetic constructMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
anti-BRIL Fab Light chainC [auth L]214Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Frizzled-5,Soluble cytochrome b562D [auth R]667Homo sapiensEscherichia coliMutation(s): 0 
Gene Names: FZD5C2orf31cybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13467 (Homo sapiens)
Explore Q13467 
Go to UniProtKB:  Q13467
PHAROS:  Q13467
GTEx:  ENSG00000163251 
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
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UniProt GroupsQ13467P0ABE7
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.12.14
MODEL REFINEMENTPHENIX1.17.1-3660

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United States1R01DK115728
Department of Energy (DOE, United States)United StatesDE-AC02-76SF00515
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release