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- PDB-9z4o: Cryo-EM structure of human Wntless in its apo state -

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Basic information

Entry
Database: PDB / ID: 9z4o
TitleCryo-EM structure of human Wntless in its apo state
ComponentsProtein wntless homolog
KeywordsMEMBRANE PROTEIN / Wnt transporter / Wnt secretion / Wnt signaling
Function / homology
Function and homology information


Wnt protein secretion / positive regulation of Wnt protein secretion / WNT ligand biogenesis and trafficking / cementum mineralization / hindbrain development / Wnt-protein binding / exocrine pancreas development / anterior/posterior axis specification / midbrain development / organelle membrane ...Wnt protein secretion / positive regulation of Wnt protein secretion / WNT ligand biogenesis and trafficking / cementum mineralization / hindbrain development / Wnt-protein binding / exocrine pancreas development / anterior/posterior axis specification / midbrain development / organelle membrane / mesoderm formation / positive regulation of Wnt signaling pathway / endomembrane system / trans-Golgi network / intracellular protein transport / Wnt signaling pathway / endocytic vesicle membrane / positive regulation of canonical Wnt signaling pathway / cytoplasmic vesicle / early endosome membrane / early endosome / positive regulation of canonical NF-kappaB signal transduction / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / extracellular exosome / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Protein wntless / : / : / Wntless-like, transmembrane domain / Wntless, GOLD domain
Similarity search - Domain/homology
Protein wntless homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.63 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 10, 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: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / 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: Mask / Part number: 1 / Data content type: Mask / 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

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Assembly

Deposited unit
A: Protein wntless homolog


Theoretical massNumber of molelcules
Total (without water)66,0881
Polymers66,0881
Non-polymers00
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

#1: 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.: 1
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
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 in nanodiscs / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
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: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86035 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 60.77 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00274038
ELECTRON MICROSCOPYf_angle_d0.54565470
ELECTRON MICROSCOPYf_chiral_restr0.0413599
ELECTRON MICROSCOPYf_plane_restr0.004669
ELECTRON MICROSCOPYf_dihedral_angle_d4.2869510

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