7DRT | pdb_00007drt

Human Wntless in complex with Wnt3a

• PDB DOI: https://doi.org/10.2210/pdb7DRT/pdb
• EM Map EMD-30827: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2020-12-29 Released: 2021-07-14 
• Deposition Author(s): Zhong, Q., Zhao, Y., Ye, F., Xiao, Z., Huang, G., Zhang, Y., Lu, P., Xu, W., Zhou, Q., Ma, D.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

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

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

• PubMed: 34315898 
• DOI: https://doi.org/10.1038/s41467-021-24731-3
• Primary Citation 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.

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Organizational Affiliation: 
• Fudan University, Shanghai, China.
Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Mass Spectrometry Core Facility, The Biomedical Research Core Facility, Center for Research Equipment and Facilities, Westlake University, Hangzhou, Zhejiang, China.
Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China. [e-mail].
Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China. [e-mail].
Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China. [e-mail].
Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China. [e-mail].
Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China. [e-mail].
Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 104.89 kDa 
• Atom Count: 6,849 
• Modeled Residue Count: 830 
• Deposited Residue Count: 893 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Wnt-3a	A	352	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein wntless homolog	B	541	Homo sapiens	Mutation(s): 0  Gene Names: WLS, C1orf139, GPR177, UNQ85/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

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth H]	2		N/A
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PCW	E [auth A], H [auth B]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H85 N O8 P SNKAWJBJQDLSFF-NVKMUCNASA-O
LPE	G [auth B]	1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE C26 H57 N O6 P XKBJVQHMEXMFDZ-AREMUKBSSA-O
CLR	F [auth B]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
PAM	D [auth A]	PALMITOLEIC ACID C16 H30 O2 SECPZKHBENQXJG-FPLPWBNLSA-N

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0.6

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Zhong, Q., Zhao, Y., Ye, F., Xiao, Z., Huang, G., Zhang, Y., Lu, P., Xu, W., Zhou, Q., Ma, D.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31971123

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2021-09-08
  Changes: Database references
• Version 1.2: 2024-10-30
  Changes: Data collection, Structure summary