7DRT

Human Wntless in complex with Wnt3a


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of human Wntless in complex with Wnt3a.

Zhong, Q.Zhao, Y.Ye, F.Xiao, Z.Huang, G.Xu, M.Zhang, Y.Zhan, X.Sun, K.Wang, Z.Cheng, S.Feng, S.Zhao, X.Zhang, J.Lu, P.Xu, W.Zhou, Q.Ma, D.

(2021) Nat Commun 12: 4541-4541

  • DOI: https://doi.org/10.1038/s41467-021-24731-3
  • Primary Citation of Related Structures:  
    7DRT

  • PubMed Abstract: 

    Wntless (WLS), an evolutionarily conserved multi-pass transmembrane protein, is essential for secretion of Wnt proteins. Wnt-triggered signaling pathways control many crucial life events, whereas aberrant Wnt signaling is tightly associated with many human diseases including cancers. Here, we report the cryo-EM structure of human WLS in complex with Wnt3a, the most widely studied Wnt, at 2.2 Å resolution. The transmembrane domain of WLS bears a GPCR fold, with a conserved core cavity and a lateral opening. Wnt3a interacts with WLS at multiple interfaces, with the lipid moiety on Wnt3a traversing a hydrophobic tunnel of WLS transmembrane domain and inserting into membrane. A β-hairpin of Wnt3a containing the conserved palmitoleoylation site interacts with WLS extensively, which is crucial for WLS-mediated Wnt secretion. The flexibility of the Wnt3a loop/hairpin regions involved in the multiple binding sites indicates induced fit might happen when Wnts are bound to different binding partners. Our findings provide important insights into the molecular mechanism of Wnt palmitoleoylation, secretion and signaling.


  • Organizational Affiliation

    Fudan University, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein Wnt-3a352Homo sapiensMutation(s): 0 
Gene Names: WNT3A
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P56704 (Homo sapiens)
Explore P56704 
Go to UniProtKB:  P56704
PHAROS:  P56704
GTEx:  ENSG00000154342 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56704
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein wntless homolog541Homo sapiensMutation(s): 0 
Gene Names: WLSC1orf139GPR177UNQ85/PRO18667
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T9L3 (Homo sapiens)
Explore Q5T9L3 
Go to UniProtKB:  Q5T9L3
PHAROS:  Q5T9L3
GTEx:  ENSG00000116729 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5T9L3
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth H]2N/A
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.6

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31971123

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2021-09-08
    Changes: Database references