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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


Wnt signaling pathway involved in forebrain neuroblast division / positive regulation of dermatome development / axis elongation involved in somitogenesis / calcium ion transmembrane transport via low voltage-gated calcium channel / : / positive regulation of collateral sprouting in absence of injury / positive regulation of mesodermal cell fate specification / paraxial mesodermal cell fate commitment / Specification of the neural plate border / cell proliferation in midbrain ...Wnt signaling pathway involved in forebrain neuroblast division / positive regulation of dermatome development / axis elongation involved in somitogenesis / calcium ion transmembrane transport via low voltage-gated calcium channel / : / positive regulation of collateral sprouting in absence of injury / positive regulation of mesodermal cell fate specification / paraxial mesodermal cell fate commitment / Specification of the neural plate border / cell proliferation in midbrain / spinal cord association neuron differentiation / Formation of the posterior neural plate / Wnt protein secretion / Calnexin/calreticulin cycle / COP9 signalosome assembly / cytolytic granule / Wnt-Frizzled-LRP5/6 complex / positive regulation of cell-cell adhesion mediated by cadherin / positive regulation of Wnt protein secretion / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / positive regulation of dendritic cell chemotaxis / synaptic vesicle recycling / Signaling by RNF43 mutants / WNT ligand biogenesis and trafficking / positive regulation of cardiac muscle cell differentiation / cortical granule / Assembly of Viral Components at the Budding Site / negative regulation of trophoblast cell migration / ATF6 (ATF6-alpha) activates chaperone genes / cell proliferation in forebrain / negative regulation of retinoic acid receptor signaling pathway / complement component C1q complex binding / endoplasmic reticulum quality control compartment / cellular response to electrical stimulus / intracellular glucocorticoid receptor signaling pathway / regulation of meiotic nuclear division / secondary palate development / negative regulation of axon extension involved in axon guidance / sequestering of calcium ion / cementum mineralization / response to glycoside / somatic stem cell division / non-canonical Wnt signaling pathway / co-receptor binding / cardiac muscle cell fate commitment / sarcoplasmic reticulum lumen / hormone binding / presynapse assembly / protein folding in endoplasmic reticulum / hindbrain development / positive regulation of skeletal muscle tissue development / nuclear export signal receptor activity / dorsal/ventral neural tube patterning / negative regulation of dopaminergic neuron differentiation / Wnt-protein binding / negative regulation of intracellular steroid hormone receptor signaling pathway / midbrain dopaminergic neuron differentiation / regulation of postsynapse to nucleus signaling pathway / cardiac muscle cell differentiation / molecular sequestering activity / post-anal tail morphogenesis / exocrine pancreas development / mammary gland development / positive regulation of neural precursor cell proliferation / frizzled binding / positive regulation of hepatocyte proliferation / Class B/2 (Secretin family receptors) / myoblast differentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / anterior/posterior axis specification / protein maturation by protein folding / Scavenging by Class F Receptors / Scavenging by Class A Receptors / cortical actin cytoskeleton organization / nuclear androgen receptor binding / inner ear morphogenesis / midbrain development / regulation of synapse organization / negative regulation of fat cell differentiation / response to testosterone / cellular response to lithium ion / fat cell differentiation / heart looping / B cell proliferation / Formation of paraxial mesoderm / ERAD pathway / skeletal muscle cell differentiation / positive regulation of receptor internalization / hemopoiesis / regulation of presynapse assembly / protein localization to nucleus / mesoderm formation / positive regulation of Wnt signaling pathway / negative regulation of neuron differentiation / smooth endoplasmic reticulum / canonical Wnt signaling pathway / cell fate commitment / endomembrane system / positive regulation of cell cycle / regulation of microtubule cytoskeleton organization
Similarity search - Function
Wnt-3 protein / Protein wntless / : / Wntless-like, transmembrane domain / Wnt protein, conserved site / Wnt-1 family signature. / Wnt / Wnt, C-terminal domain / wnt family / found in Wnt-1 ...Wnt-3 protein / Protein wntless / : / Wntless-like, transmembrane domain / Wnt protein, conserved site / Wnt-1 family signature. / Wnt / Wnt, C-terminal domain / wnt family / found in Wnt-1 / Calreticulin / Calreticulin family repeated motif signature. / 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: To Be Published
Title: Structure of human Wnt3a bound to WLS and CALR
Authors: Qi X / Hu Q / Li X
History
DepositionAug 27, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing 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)
Voxel sizeX=Y=Z: 0.83 Å
Density
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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41767_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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 / 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 / POPC

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

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 113802

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