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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 / hypophysis morphogenesis / positive regulation of timing of anagen / cervix development / positive regulation of protein kinase C activity / negative regulation of cell proliferation in midbrain / primary heart field specification / chemorepulsion of dopaminergic neuron axon ...optic cup formation involved in camera-type eye development / receptor tyrosine kinase-like orphan receptor binding / chemoattraction of serotonergic neuron axon / hypophysis morphogenesis / positive regulation of timing of anagen / cervix development / positive regulation of protein kinase C activity / negative regulation of cell proliferation in midbrain / primary heart field specification / chemorepulsion of dopaminergic neuron axon / mesodermal to mesenchymal transition involved in gastrulation / negative regulation of prostatic bud formation / postsynapse assembly / olfactory bulb interneuron development / chemoattractant activity involved in axon guidance / melanocyte proliferation / convergent extension involved in organogenesis / mesenchymal-epithelial cell signaling / negative regulation of melanin biosynthetic process / notochord morphogenesis / paraxial mesoderm formation / meiotic nuclear division / Wnt signaling pathway, calcium modulating pathway / regulation of postsynaptic cytosolic calcium ion concentration / convergent extension involved in axis elongation / urinary bladder development / Wnt protein secretion / positive regulation of hematopoietic stem cell proliferation / negative regulation of synapse assembly / negative regulation of mesenchymal cell proliferation / hindgut morphogenesis / macrophage derived foam cell differentiation / epithelial cell migration / regulation of branching involved in mammary gland duct morphogenesis / positive regulation of Wnt protein secretion / positive regulation of non-canonical Wnt signaling pathway / secondary heart field specification / negative regulation of axon extension involved in axon guidance / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / primitive streak formation / WNT ligand biogenesis and trafficking / positive regulation of cell-cell adhesion mediated by cadherin / negative regulation of fibroblast growth factor receptor signaling pathway / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / excitatory synapse assembly / positive regulation of cartilage development / anterior/posterior axis specification, embryo / axon extension involved in axon guidance / establishment of planar polarity / midgut development / WNT5A-dependent internalization of FZD4 / lateral sprouting involved in mammary gland duct morphogenesis / cementum mineralization / secondary palate development / positive regulation of neuron projection arborization / presynapse assembly / positive regulation of meiotic nuclear division / positive regulation of T cell chemotaxis / embryonic skeletal system development / pericardium morphogenesis / mammary gland branching involved in thelarche / genitalia development / type B pancreatic cell development / mesenchymal cell proliferation / hindbrain development / non-canonical Wnt signaling pathway / cochlea morphogenesis / Wnt-protein binding / positive regulation of cytokine production involved in immune response / atrial septum development / WNT5:FZD7-mediated leishmania damping / post-anal tail morphogenesis / positive regulation of response to cytokine stimulus / establishment of epithelial cell apical/basal polarity / midbrain dopaminergic neuron differentiation / positive regulation of macrophage activation / exocrine pancreas development / frizzled binding / positive regulation of ossification / positive regulation of type I interferon-mediated signaling pathway / PCP/CE pathway / Class B/2 (Secretin family receptors) / positive regulation of thymocyte apoptotic process / cartilage development / inhibitory synapse assembly / lens development in camera-type eye / regulation of canonical NF-kappaB signal transduction / regulation of postsynapse organization / anterior/posterior axis specification / Wnt signaling pathway, planar cell polarity pathway / positive regulation of mesenchymal cell proliferation / positive regulation of macrophage cytokine production / embryonic digit morphogenesis / ventricular septum development / thymocyte apoptotic process / epithelial cell proliferation involved in mammary gland duct elongation / positive regulation of protein localization to synapse / negative regulation of fat cell differentiation / hematopoietic stem cell proliferation / heart looping
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: To Be Published
Title: Conformational cycling of the Wntless transporter drives trafficking and secretion of Wnt morphogens
Authors: Ge, Y. / de Almeida Magalhaes, T. / Wu, H. / van den Boomen, D.J.H. / Nguyen, T.U. / Dou, T. / Yadav, G.P. / Lee, S. / Wang, Z. / Lemoff, A. / Luo, X. / Jin, Z. / Jiang, J. / Salic, A. / Huang, P.
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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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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