8TZR | pdb_00008tzr

Structure of human Wnt3a bound to WLS and CALR

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

  • Deposited: 2023-08-27 Released: 2023-10-18 
  • Deposition Author(s): Qi, X., Hu, Q., Li, X.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8TZR

This is version 1.3 of the entry. See complete history

Literature

Molecular basis of Wnt biogenesis, secretion, and Wnt7-specific signaling.

Qi, X.Hu, Q.Elghobashi-Meinhardt, N.Long, T.Chen, H.Li, X.

(2023) Cell 186: 5028-5040.e14

  • DOI: https://doi.org/10.1016/j.cell.2023.09.021
  • Primary Citation Related Structures: 
    8TZO, 8TZP, 8TZR, 8TZS

  • PubMed Abstract: 

    Wnt proteins are enzymatically lipidated by Porcupine (PORCN) in the ER and bind to Wntless (WLS) for intracellular transport and secretion. Mechanisms governing the transfer of these low-solubility Wnts from the ER to the extracellular space remain unclear. Through structural and functional analyses of Wnt7a, a crucial Wnt involved in central nervous system angiogenesis and blood-brain barrier maintenance, we have elucidated the principles of Wnt biogenesis and Wnt7-specific signaling. The Wnt7a-WLS complex binds to calreticulin (CALR), revealing that CALR functions as a chaperone to facilitate Wnt transfer from PORCN to WLS during Wnt biogenesis. Our structures, functional analyses, and molecular dynamics simulations demonstrate that a phospholipid in the core of Wnt-bound WLS regulates the association and dissociation between Wnt and WLS, suggesting a lipid-mediated Wnt secretion mechanism. Finally, the structure of Wnt7a bound to RECK, a cell-surface Wnt7 co-receptor, reveals how RECK CC4 engages the N-terminal domain of Wnt7a to activate Wnt7-specific signaling.


  • Organizational Affiliation
    • Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address: xiaofeng.qi@utsouthwestern.edu.

Macromolecule Content 

  • Total Structure Weight: 152.19 kDa 
  • Atom Count: 8,821 
  • Modeled Residue Count: 1,079 
  • Deposited Residue Count: 1,310 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P56704-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein wntless homolog541Homo sapiensMutation(s): 0 
Gene Names: WLS
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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Calreticulin417Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P27797 (Homo sapiens)
Explore P27797 
Go to UniProtKB:  P27797
PHAROS:  P27797
GTEx:  ENSG00000179218 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27797
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G85146YR
GlyCosmos: G85146YR
GlyGen: G85146YR

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV
(Subject of Investigation/LOI)

Query on POV



Download:Ideal Coordinates CCD File
F [auth B](2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
PAM
(Subject of Investigation/LOI)

Query on PAM



Download:Ideal Coordinates CCD File
E [auth A]PALMITOLEIC ACID
C16 H30 O2
SECPZKHBENQXJG-FPLPWBNLSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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 StatesGM135343
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesHL160487
Welch FoundationUnited StatesI-1957

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-18
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references
  • Version 1.3: 2025-06-04
    Changes: Data collection