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- EMDB-73810: Cryo-EM structure of human Wntless in its apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-73810
TitleCryo-EM structure of human Wntless in its apo state
Map datastructure of human Wntless in its apo state
Sample
  • Complex: human Wntless in nanodiscs
    • Protein or peptide: Protein wntless homolog
KeywordsWnt transporter / Wnt secretion / Wnt signaling / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsGe Y / de Almeida Magalhaes T / Wu H / Yadav GP / Wang Z / Salic A / Jiang J / Huang P
Funding support United States, 1 items
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 DJH / Nguyen TU / Dou T / Yadav GP / Lee S / Wang Z / Lemoff A / Luo X / Jin Z / Jiang J / Salic A / Huang P
History
DepositionNov 10, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73810.png

Downloads & links

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Map

FileDownload / File: emd_73810.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of human Wntless in its apo state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-1.1606781 - 1.6438829
Average (Standard dev.)0.00075721694 (±0.021934388)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73810_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_73810_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_73810_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human Wntless in nanodiscs

EntireName: human Wntless in nanodiscs
Components
  • Complex: human Wntless in nanodiscs
    • Protein or peptide: Protein wntless homolog

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Supramolecule #1: human Wntless in nanodiscs

SupramoleculeName: human Wntless in nanodiscs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein wntless homolog

MacromoleculeName: Protein wntless homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.088141 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGAIIENMS TKKLCIVGGI LLVFQIIAFL VGGLIAPGPT TAVSYMSVKC VDARKNHHKT KWFVPWGPNH CDKIRDIEEA IPREIEAND IVFSVHIPLP HMEMSPWFQF MLFILQLDIA FKLNNQIREN AEVSMDVSLA YRDDAFAEWT EMAHERVPRK L KCTFTSPK ...String:
MAGAIIENMS TKKLCIVGGI LLVFQIIAFL VGGLIAPGPT TAVSYMSVKC VDARKNHHKT KWFVPWGPNH CDKIRDIEEA IPREIEAND IVFSVHIPLP HMEMSPWFQF MLFILQLDIA FKLNNQIREN AEVSMDVSLA YRDDAFAEWT EMAHERVPRK L KCTFTSPK TPEHEGRYYE CDVLPFMEIG SVAHKFYLLN IRLPVNEKKK INVGIGEIKD IRLVGIHQNG GFTKVWFAMK TF LTPSIFI IMVWYWRRIT MMSRPPVLLE KVIFALGISM TFINIPVEWF SIGFDWTWML LFGDIRQGIF YAMLLSFWII FCG EHMMDQ HERNHIAGYW KQVGPIAVGS FCLFIFDMCE RGVQLTNPFY SIWTTDIGTE LAMAFIIVAG ICLCLYFLFL CFMV FQVFR NISGKQSSLP AMSKVRRLHY EGLIFRFKFL MLITLACAAM TVIFFIVSQV TEGHWKWGGV TVQVNSAFFT GIYGM WNLY VFALMFLYAP SHKNYGEDQS NGDLGVHSGE ELQLTTTITH VDGPTEIYKL TRKEAQEAAA LEVLFQGPGA AEDQVD PRL IDGKHHHHHH HH

UniProtKB: Protein wntless homolog

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.83 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 86035
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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