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- EMDB-41767: Structure of human Wnt3a bound to WLS and CALR -

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Basic information

Entry
Database: EMDB / ID: EMD-41767
TitleStructure of human Wnt3a bound to WLS and CALR
Map data
Sample
  • Complex: Wnt3a-WLS-CALR Complex
    • Protein or peptide: Protein Wnt-3a
    • Protein or peptide: Protein wntless homolog
    • Protein or peptide: Calreticulin
  • Ligand: PALMITOLEIC ACID
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


cell proliferation in midbrain / positive regulation of dermatome development / calcium ion transmembrane transport via low voltage-gated calcium channel / positive regulation of mesodermal cell fate specification / response to biphenyl / negative regulation of intracellular steroid hormone receptor signaling pathway / Formation of the posterior neural plate / Wnt protein secretion / Calnexin/calreticulin cycle / cytolytic granule ...cell proliferation in midbrain / positive regulation of dermatome development / calcium ion transmembrane transport via low voltage-gated calcium channel / positive regulation of mesodermal cell fate specification / response to biphenyl / negative regulation of intracellular steroid hormone receptor signaling pathway / Formation of the posterior neural plate / Wnt protein secretion / Calnexin/calreticulin cycle / cytolytic granule / Wnt-Frizzled-LRP5/6 complex / positive regulation of Wnt protein secretion / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / nuclear receptor-mediated glucocorticoid signaling pathway / positive regulation of dendritic cell chemotaxis / Signaling by RNF43 mutants / Assembly of Viral Components at the Budding Site / COP9 signalosome assembly / cell proliferation in forebrain / WNT ligand biogenesis and trafficking / ATF6 (ATF6-alpha) activates chaperone genes / cellular response to electrical stimulus / negative regulation of trophoblast cell migration / Specification of the neural plate border / negative regulation of retinoic acid receptor signaling pathway / positive regulation of skeletal muscle tissue development / cortical granule / anterior/posterior axis specification / cementum mineralization / response to peptide / complement component C1q complex binding / secondary palate development / endoplasmic reticulum quality control compartment / exocrine pancreas development / presynapse assembly / cardiac muscle cell fate commitment / hindbrain development / sarcoplasmic reticulum lumen / synaptic vesicle recycling / protein folding in endoplasmic reticulum / non-canonical Wnt signaling pathway / co-receptor binding / cellular response to lithium ion / negative regulation of dopaminergic neuron differentiation / Wnt-protein binding / regulation of postsynapse to nucleus signaling pathway / nuclear export signal receptor activity / cardiac muscle cell differentiation / positive regulation of cardiac muscle cell differentiation / midbrain dopaminergic neuron differentiation / mesoderm formation / frizzled binding / response to glycoside / Class B/2 (Secretin family receptors) / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of neuron differentiation / Scavenging by Class A Receptors / midbrain development / Scavenging by Class F Receptors / nuclear androgen receptor binding / response to testosterone / Formation of paraxial mesoderm / cell fate commitment / regulation of synapse organization / organelle membrane / canonical Wnt signaling pathway / smooth endoplasmic reticulum / hormone binding / positive regulation of receptor internalization / protein localization to nucleus / positive regulation of substrate adhesion-dependent cell spreading / molecular sequestering activity / protein export from nucleus / positive regulation of Wnt signaling pathway / regulation of presynapse assembly / cellular response to retinoic acid / endocytic vesicle lumen / peptide binding / ERAD pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of cell cycle / endomembrane system / positive regulation of endothelial cell migration / protein folding chaperone / positive regulation of phagocytosis / acrosomal vesicle / cytokine activity / Regulation of FZD by ubiquitination / positive regulation of protein localization to plasma membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / negative regulation of neuron projection development / lumenal side of endoplasmic reticulum membrane / TCF dependent signaling in response to WNT / cellular response to virus / protein maturation / Maturation of DENV proteins / trans-Golgi network / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex
Similarity search - Function
Wnt-3 protein / Protein wntless / : / : / Wntless-like, transmembrane domain / Wntless, GOLD domain / Calreticulin / Wnt protein, conserved site / Wnt-1 family signature. / Calreticulin family repeated motif signature. ...Wnt-3 protein / Protein wntless / : / : / Wntless-like, transmembrane domain / Wntless, GOLD domain / Calreticulin / Wnt protein, conserved site / Wnt-1 family signature. / Calreticulin family repeated motif signature. / Wnt / Wnt, C-terminal domain / wnt family / found in Wnt-1 / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. / Endoplasmic reticulum targeting sequence. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Calreticulin / Protein Wnt-3a / Protein wntless homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsQi X / Hu Q / Li X
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135343 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)HL160487 United States
Welch FoundationI-1957 United States
CitationJournal: Cell / Year: 2023
Title: Molecular basis of Wnt biogenesis, secretion, and Wnt7-specific signaling.
Authors: Xiaofeng Qi / Qinli Hu / Nadia Elghobashi-Meinhardt / Tao Long / Hongwen Chen / Xiaochun Li /
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 ...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 engages the N-terminal domain of Wnt7a to activate Wnt7-specific signaling.
History
DepositionAug 27, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41767.png

Downloads & links

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Map

FileDownload / File: emd_41767.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 280 pix.
= 232.4 Å		0.83 Å/pix.
x 280 pix.
= 232.4 Å		0.83 Å/pix.
x 280 pix.
= 232.4 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.287
Minimum - Maximum-1.9777877 - 2.942259
Average (Standard dev.)0.005658618 (±0.060342725)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 232.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41767_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41767_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Wnt3a-WLS-CALR Complex

EntireName: Wnt3a-WLS-CALR Complex
Components
  • Complex: Wnt3a-WLS-CALR Complex
    • Protein or peptide: Protein Wnt-3a
    • Protein or peptide: Protein wntless homolog
    • Protein or peptide: Calreticulin
  • Ligand: PALMITOLEIC ACID
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate

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Supramolecule #1: Wnt3a-WLS-CALR Complex

SupramoleculeName: Wnt3a-WLS-CALR Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein Wnt-3a

MacromoleculeName: Protein Wnt-3a / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.421832 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAPLGYFLLL CSLKQALGSY PIWWSLAVGP QYSSLGSQPI LCASIPGLVP KQLRFCRNYV EIMPSVAEGI KIGIQECQHQ FRGRRWNCT TVHDSLAIFG PVLDKATRES AFVHAIASAG VAFAVTRSCA EGTAAICGCS SRHQGSPGKG WKWGGCSEDI E FGGMVSRE ...String:
MAPLGYFLLL CSLKQALGSY PIWWSLAVGP QYSSLGSQPI LCASIPGLVP KQLRFCRNYV EIMPSVAEGI KIGIQECQHQ FRGRRWNCT TVHDSLAIFG PVLDKATRES AFVHAIASAG VAFAVTRSCA EGTAAICGCS SRHQGSPGKG WKWGGCSEDI E FGGMVSRE FADARENRPD ARSAMNRHNN EAGRQAIASH MHLKCKCHGL SGSCEVKTCW WSQPDFRAIG DFLKDKYDSA SE MVVEKHR ESRGWVETLR PRYTYFKVPT ERDLVYYEAS PNFCEPNPET GSFGTRDRTC NVSSHGIDGC DLLCCGRGHN ARA ERRREK CRCVFHWCCY VSCQECTRVY DVHTCK

UniProtKB: Protein Wnt-3a

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Macromolecule #2: Protein wntless homolog

MacromoleculeName: Protein wntless homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.317973 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 TRKEAQE

UniProtKB: Protein wntless homolog

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Macromolecule #3: Calreticulin

MacromoleculeName: Calreticulin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.198379 KDa
SequenceString: MLLSVPLLLG LLGLAVAEPA VYFKEQFLDG DGWTSRWIES KHKSDFGKFV LSSGKFYGDE EKDKGLQTSQ DARFYALSAS FEPFSNKGQ TLVVQFTVKH EQNIDCGGGY VKLFPNSLDQ TDMHGDSEYN IMFGPDICGP GTKKVHVIFN YKGKNVLINK D IRCKDDEF ...String:
MLLSVPLLLG LLGLAVAEPA VYFKEQFLDG DGWTSRWIES KHKSDFGKFV LSSGKFYGDE EKDKGLQTSQ DARFYALSAS FEPFSNKGQ TLVVQFTVKH EQNIDCGGGY VKLFPNSLDQ TDMHGDSEYN IMFGPDICGP GTKKVHVIFN YKGKNVLINK D IRCKDDEF THLYTLIVRP DNTYEVKIDN SQVESGSLED DWDFLPPKKI KDPDASKPED WDERAKIDDP TDSKPEDWDK PE HIPDPDA KKPEDWDEEM DGEWEPPVIQ NPEYKGEWKP RQIDNPDYKG TWIHPEIDNP EYSPDPSIYA YDNFGVLGLD LWQ VKSGTI FDNFLITNDE AYAEEFGNET WGVTKAAEKQ MKDKQDEEQR LKEEEEDKKR KEEEEAEDKE DDEDKDEDEE DEED KEEDE EEDVPGQAKD EL

UniProtKB: Calreticulin

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Macromolecule #5: PALMITOLEIC ACID

MacromoleculeName: PALMITOLEIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: PAM
Molecular weightTheoretical: 254.408 Da
Chemical component information

ChemComp-PAM:
PALMITOLEIC ACID

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Macromolecule #6: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 6 / Number of copies: 1 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 113802
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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