7KC4

Human WLS in complex with WNT8A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis of WLS/Evi-Mediated Wnt Transport and Secretion.

Nygaard, R.Yu, J.Kim, J.Ross, D.R.Parisi, G.Clarke, O.B.Virshup, D.M.Mancia, F.

(2021) Cell 184: 194

  • DOI: 10.1016/j.cell.2020.11.038
  • Primary Citation of Related Structures:  
    7KC4

  • PubMed Abstract: 
  • Wnts are evolutionarily conserved ligands that signal at short range to regulate morphogenesis, cell fate, and stem cell renewal. The first and essential steps in Wnt secretion are their O-palmitoleation and subsequent loading onto the dedicated transporter Wntless/evenness interrupted (WLS/Evi) ...

    Wnts are evolutionarily conserved ligands that signal at short range to regulate morphogenesis, cell fate, and stem cell renewal. The first and essential steps in Wnt secretion are their O-palmitoleation and subsequent loading onto the dedicated transporter Wntless/evenness interrupted (WLS/Evi). We report the 3.2 Å resolution cryogenic electron microscopy (cryo-EM) structure of palmitoleated human WNT8A in complex with WLS. This is accompanied by biochemical experiments to probe the physiological implications of the observed association. The WLS membrane domain has close structural homology to G protein-coupled receptors (GPCRs). A Wnt hairpin inserts into a conserved hydrophobic cavity in the GPCR-like domain, and the palmitoleate protrudes between two helices into the bilayer. A conformational switch of highly conserved residues on a separate Wnt hairpin might contribute to its transfer to receiving cells. This work provides molecular-level insights into a central mechanism in animal body plan development and stem cell biology.


    Organizational Affiliation

    Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA. Electronic address: fm123@cumc.columbia.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein Wnt-8aA [auth D]361Homo sapiensMutation(s): 0 
Gene Names: WNT8AWNT8D
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1J5 (Homo sapiens)
Explore Q9H1J5 
Go to UniProtKB:  Q9H1J5
PHAROS:  Q9H1J5
GTEx:  ENSG00000061492 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H1J5
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein wntless homologB567Homo 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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth A]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth C]6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42984ZU
GlyCosmos:  G42984ZU
GlyGen:  G42984ZU
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DR9
Query on DR9

Download Ideal Coordinates CCD File 
F [auth B],
G [auth B],
H [auth B]
1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL
C40 H75 O10 P
QGIXWNRQEFVVRM-CTDKCSBDSA-N
 Ligand Interaction
Y01
Query on Y01

Download Ideal Coordinates CCD File 
I [auth B]CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
 Ligand Interaction
PLM (Subject of Investigation/LOI)
Query on PLM

Download Ideal Coordinates CCD File 
E [auth D]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM132120
National Research Foundation (NRF, Singapore)SingaporeMOH-000155

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-06
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references
  • Version 1.2: 2021-01-20
    Changes: Database references