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- PDB-9z67: Cryo-EM structure of human Wntless-Wnt5a 2:2 complex - Composite map -

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Basic information

Entry
Database: PDB / ID: 9z67
TitleCryo-EM structure of human Wntless-Wnt5a 2:2 complex - Composite map
Components
  • Protein Wnt-5a
  • Protein wntless homolog
KeywordsMEMBRANE PROTEIN / Wnt transporter / Wnt secretion / Wnt5a / Wnt signaling
Function / homology
Function and homology information


optic cup formation involved in camera-type eye development / receptor tyrosine kinase-like orphan receptor binding / chemoattraction of serotonergic neuron axon / positive regulation of timing of anagen / negative regulation of cell proliferation in midbrain / primary heart field specification / chemorepulsion of dopaminergic neuron axon / postsynapse assembly / olfactory bulb interneuron development / positive regulation of protein kinase C activity ...optic cup formation involved in camera-type eye development / receptor tyrosine kinase-like orphan receptor binding / chemoattraction of serotonergic neuron axon / positive regulation of timing of anagen / negative regulation of cell proliferation in midbrain / primary heart field specification / chemorepulsion of dopaminergic neuron axon / postsynapse assembly / olfactory bulb interneuron development / positive regulation of protein kinase C activity / chemoattractant activity involved in axon guidance / melanocyte proliferation / negative regulation of mesenchymal cell proliferation / negative regulation of melanin biosynthetic process / Wnt signaling pathway, calcium modulating pathway / regulation of postsynaptic cytosolic calcium ion concentration / Wnt protein secretion / cementum mineralization / negative regulation of synapse assembly / macrophage derived foam cell differentiation / atrial septum development / positive regulation of Wnt protein secretion / secondary heart field specification / positive regulation of non-canonical Wnt signaling pathway / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT ligand biogenesis and trafficking / excitatory synapse assembly / anterior/posterior axis specification, embryo / embryonic skeletal system development / WNT5A-dependent internalization of FZD4 / positive regulation of macrophage cytokine production / face development / anterior/posterior axis specification / secondary palate development / exocrine pancreas development / positive regulation of neuron projection arborization / presynapse assembly / hindbrain development / positive regulation of T cell chemotaxis / genitalia development / ventricular septum development / non-canonical Wnt signaling pathway / Wnt-protein binding / WNT5:FZD7-mediated leishmania damping / lens development in camera-type eye / positive regulation of cytokine production involved in immune response / hematopoietic stem cell proliferation / positive regulation of response to cytokine stimulus / midbrain dopaminergic neuron differentiation / cartilage development / positive regulation of macrophage activation / mesoderm formation / positive regulation of ossification / positive regulation of type I interferon-mediated signaling pathway / PCP/CE pathway / Class B/2 (Secretin family receptors) / frizzled binding / regulation of postsynapse organization / inhibitory synapse assembly / Wnt signaling pathway, planar cell polarity pathway / regulation of canonical NF-kappaB signal transduction / negative regulation of fat cell differentiation / midbrain development / positive regulation of Rac protein signal transduction / positive regulation of protein localization to synapse / cell fate commitment / regulation of synapse organization / canonical Wnt signaling pathway / keratinocyte differentiation / epithelial to mesenchymal transition / cellular response to transforming growth factor beta stimulus / positive regulation of Wnt signaling pathway / postsynaptic modulation of chemical synaptic transmission / cellular response to retinoic acid / positive regulation of chemokine production / positive regulation of endothelial cell proliferation / endomembrane system / male gonad development / cellular response to calcium ion / positive regulation of apoptotic signaling pathway / positive regulation of endothelial cell migration / Wnt signaling pathway / axon guidance / positive regulation of fibroblast proliferation / cytokine activity / wound healing / positive regulation of interleukin-8 production / positive regulation of interleukin-1 beta production / positive regulation of neuron projection development / TCF dependent signaling in response to WNT / trans-Golgi network / clathrin-coated endocytic vesicle membrane / negative regulation of canonical Wnt signaling pathway / intracellular protein transport / Asymmetric localization of PCP proteins / cellular response to type II interferon / positive regulation of type II interferon production / phospholipid binding / positive regulation of interleukin-6 production
Similarity search - Function
Protein wntless / : / : / Wntless-like, transmembrane domain / Wntless, GOLD domain / Wnt protein, conserved site / Wnt-1 family signature. / Wnt / Wnt, C-terminal domain / wnt family / found in Wnt-1
Similarity search - Domain/homology
CHOLESTEROL / PALMITOLEIC ACID / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Protein Wnt-5a / Protein wntless homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsGe, Y. / de Almeida Magalhaes, T. / Wu, H. / Yadav, G.P. / Wang, Z. / Salic, A. / Jiang, J. / Huang, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM150878 United States
CitationJournal: Nat Commun / Year: 2026
Title: Conformational cycling of the Wntless transporter drives trafficking and secretion of Wnt morphogens.
Authors: Yunhui Ge / Taciani de Almeida Magalhaes / Hongjiang Wu / Dick J H van den Boomen / Thu Uyen Nguyen / Tongyi Dou / Gaya P Yadav / Sukyeong Lee / Zhao Wang / Andrew Lemoff / Xuemei Luo / ...Authors: Yunhui Ge / Taciani de Almeida Magalhaes / Hongjiang Wu / Dick J H van den Boomen / Thu Uyen Nguyen / Tongyi Dou / Gaya P Yadav / Sukyeong Lee / Zhao Wang / Andrew Lemoff / Xuemei Luo / Sumitha S Menon / Min Zhang / Jin Wang / Zhicheng Jin / Jiansen Jiang / Adrian Salic / Pengxiang Huang /
Abstract: Wnt proteins are lipid-modified morphogens fundamental in development and disease. During Wnt biogenesis, the G-protein-coupled receptor (GPCR)-like transporter Wntless (WLS) escorts lipidated Wnts ...Wnt proteins are lipid-modified morphogens fundamental in development and disease. During Wnt biogenesis, the G-protein-coupled receptor (GPCR)-like transporter Wntless (WLS) escorts lipidated Wnts from the endoplasmic reticulum to the plasma membrane, then transfers them to extracellular carriers, forming active and soluble morphogen-carrier complexes. To dissect the mechanisms involved, we solve cryo-EM structures of Wnt-bound WLS and unliganded WLS, and perform structure-guided functional experiments. Wnts engage WLS via three conserved hairpins, which are all required for Wnt trafficking to the cell surface and carrier-mediated secretion. Wnt release from cells is driven by dramatic conformational changes in the WLS transmembrane domain, reminiscent of GPCR activation, together with WLS extracellular rearrangements. Unexpectedly, we find that Wnt5a bound to WLS forms dimers, with implications for Wnt signaling. These findings define the mechanism of WLS conformational cycling that governs the intracellular transport and extracellular release of Wnt morphogens, essential steps in the Wnt pathway.
History
DepositionNov 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
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Revision 1.1Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein Wnt-5a
B: Protein wntless homolog
C: Protein Wnt-5a
D: Protein wntless homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,43116
Polymers209,8414
Non-polymers4,59012
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Protein Wnt-5a


Mass: 38832.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WNT5A / Production host: Homo sapiens (human) / References: UniProt: P41221
#2: Protein Protein wntless homolog / Integral membrane protein GPR177 / Protein evenness interrupted homolog / EVI / Putative NF-kappa-B- ...Integral membrane protein GPR177 / Protein evenness interrupted homolog / EVI / Putative NF-kappa-B-activating protein 373


Mass: 66088.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WLS, C1orf139, GPR177, UNQ85/PRO18667 / Production host: Homo sapiens (human) / References: UniProt: Q5T9L3

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Sugars , 2 types, 6 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 6 molecules

#4: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#7: Chemical ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human Wntless-Wnt5a 2:2 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50.83 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2PHENIX1.20_4459:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.32 Å / Resolution method: OTHER / Num. of particles: 174062 / Symmetry type: POINT
RefinementCross valid method: NONE

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