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- EMDB-30827: Human Wntless in complex with Wnt3a -

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Basic information

Entry
Database: EMDB / ID: EMD-30827
TitleHuman Wntless in complex with Wnt3a
Map data2.2_angstrom_map for WLS-Wnt3a complex
Sample
  • Complex: Human Wntless in complex with Wnt3a
    • Complex: Wnt3a
      • Protein or peptide: Protein Wnt-3a
    • Complex: Wntless
      • Protein or peptide: Protein wntless homolog
  • Ligand: PALMITOLEIC ACID
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: CHOLESTEROL
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: water
KeywordsWnt signaling / Wnt secretion / WLS / Wnt3a / cryo-EM / palmitoleoylation / membrane protein
Function / homology
Function and homology information


Wnt signaling pathway involved in forebrain neuroblast division / positive regulation of dermatome development / 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 / axis elongation involved in somitogenesis / cell proliferation in midbrain / spinal cord association neuron differentiation / Wnt protein secretion ...Wnt signaling pathway involved in forebrain neuroblast division / positive regulation of dermatome development / 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 / axis elongation involved in somitogenesis / cell proliferation in midbrain / spinal cord association neuron differentiation / Wnt protein secretion / Formation of the posterior neural plate / COP9 signalosome assembly / 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 / synaptic vesicle recycling / WNT ligand biogenesis and trafficking / Signaling by RNF43 mutants / positive regulation of cardiac muscle cell differentiation / cell proliferation in forebrain / negative regulation of axon extension involved in axon guidance / secondary palate development / Specification of the neural plate border / cementum mineralization / somatic stem cell division / cardiac muscle cell fate commitment / co-receptor binding / presynapse assembly / non-canonical Wnt signaling pathway / hindbrain development / positive regulation of skeletal muscle tissue development / negative regulation of dopaminergic neuron differentiation / Wnt-protein binding / midbrain dopaminergic neuron differentiation / dorsal/ventral neural tube patterning / regulation of postsynapse to nucleus signaling pathway / exocrine pancreas development / mammary gland development / post-anal tail morphogenesis / positive regulation of neural precursor cell proliferation / frizzled binding / Class B/2 (Secretin family receptors) / positive regulation of hepatocyte proliferation / myoblast differentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / anterior/posterior axis specification / inner ear morphogenesis / midbrain development / regulation of synapse organization / negative regulation of fat cell differentiation / organelle membrane / B cell proliferation / fat cell differentiation / heart looping / Formation of paraxial mesoderm / skeletal muscle cell differentiation / positive regulation of receptor internalization / hemopoiesis / mesoderm formation / regulation of presynapse assembly / positive regulation of Wnt signaling pathway / cell fate commitment / canonical Wnt signaling pathway / endomembrane system / Transcriptional and post-translational regulation of MITF-M expression and activity / regulation of microtubule cytoskeleton organization / positive regulation of B cell proliferation / cellular response to retinoic acid / Regulation of FZD by ubiquitination / extracellular matrix organization / axon guidance / positive regulation of cytokine production / cytokine activity / TCF dependent signaling in response to WNT / hippocampus development / positive regulation of protein localization to plasma membrane / intracellular protein transport / trans-Golgi network / modulation of chemical synaptic transmission / neuron differentiation / platelet aggregation / Wnt signaling pathway / negative regulation of neurogenesis / Golgi lumen / osteoblast differentiation / endocytic vesicle membrane / protein localization / positive regulation of canonical Wnt signaling pathway / negative regulation of neuron projection development / positive regulation of peptidyl-serine phosphorylation / presynapse / heart development / early endosome membrane / cytoplasmic vesicle / positive regulation of canonical NF-kappaB signal transduction / in utero embryonic development / transcription by RNA polymerase II / cell population proliferation / transcription coactivator activity
Similarity search - Function
Wnt-3 protein / Protein wntless / : / : / Wntless-like, transmembrane domain / Wntless, GOLD domain / Wnt protein, conserved site / Wnt-1 family signature. / Wnt / Wnt, C-terminal domain ...Wnt-3 protein / 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
Protein Wnt-3a / Protein wntless homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsZhong Q / Zhao Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971123 China
CitationJournal: Nat Commun / Year: 2021
Title: Cryo-EM structure of human Wntless in complex with Wnt3a.
Authors: Qing Zhong / Yanyu Zhao / Fangfei Ye / Zaiyu Xiao / Gaoxingyu Huang / Meng Xu / Yuanyuan Zhang / Xiechao Zhan / Ke Sun / Zhizhi Wang / Shanshan Cheng / Shan Feng / Xiuxiu Zhao / Jizhong ...Authors: Qing Zhong / Yanyu Zhao / Fangfei Ye / Zaiyu Xiao / Gaoxingyu Huang / Meng Xu / Yuanyuan Zhang / Xiechao Zhan / Ke Sun / Zhizhi Wang / Shanshan Cheng / Shan Feng / Xiuxiu Zhao / Jizhong Zhang / Peilong Lu / Wenqing Xu / Qiang Zhou / Dan Ma /
Abstract: Wntless (WLS), an evolutionarily conserved multi-pass transmembrane protein, is essential for secretion of Wnt proteins. Wnt-triggered signaling pathways control many crucial life events, whereas ...Wntless (WLS), an evolutionarily conserved multi-pass transmembrane protein, is essential for secretion of Wnt proteins. Wnt-triggered signaling pathways control many crucial life events, whereas aberrant Wnt signaling is tightly associated with many human diseases including cancers. Here, we report the cryo-EM structure of human WLS in complex with Wnt3a, the most widely studied Wnt, at 2.2 Å resolution. The transmembrane domain of WLS bears a GPCR fold, with a conserved core cavity and a lateral opening. Wnt3a interacts with WLS at multiple interfaces, with the lipid moiety on Wnt3a traversing a hydrophobic tunnel of WLS transmembrane domain and inserting into membrane. A β-hairpin of Wnt3a containing the conserved palmitoleoylation site interacts with WLS extensively, which is crucial for WLS-mediated Wnt secretion. The flexibility of the Wnt3a loop/hairpin regions involved in the multiple binding sites indicates induced fit might happen when Wnts are bound to different binding partners. Our findings provide important insights into the molecular mechanism of Wnt palmitoleoylation, secretion and signaling.
History
DepositionDec 29, 2020-
Header (metadata) releaseJul 14, 2021-
Map releaseJul 14, 2021-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7drt
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30827.png

Downloads & links

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Map

FileDownload / File: emd_30827.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation2.2_angstrom_map for WLS-Wnt3a complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.54 Å/pix.
x 512 pix.
= 278.272 Å		0.54 Å/pix.
x 512 pix.
= 278.272 Å		0.54 Å/pix.
x 512 pix.
= 278.272 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.5435 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.25
Minimum - Maximum-4.23394 - 9.254435000000001
Average (Standard dev.)-0.00030710245 (±0.05671689)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 278.272 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.54350.54350.5435
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z278.272278.272278.272
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-4.2349.254-0.000

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Supplemental data

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Additional map: 3.2 angstrom map for WLS-Wnt3a complex

Fileemd_30827_additional_1.map
Annotation3.2_angstrom_map for WLS-Wnt3a complex
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 complex with Wnt3a

EntireName: Human Wntless in complex with Wnt3a
Components
  • Complex: Human Wntless in complex with Wnt3a
    • Complex: Wnt3a
      • Protein or peptide: Protein Wnt-3a
    • Complex: Wntless
      • Protein or peptide: Protein wntless homolog
  • Ligand: PALMITOLEIC ACID
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: CHOLESTEROL
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: water

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Supramolecule #1: Human Wntless in complex with Wnt3a

SupramoleculeName: Human Wntless in complex with Wnt3a / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Wnt3a

SupramoleculeName: Wnt3a / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Wntless

SupramoleculeName: Wntless / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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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 #4: PALMITOLEIC ACID

MacromoleculeName: PALMITOLEIC ACID / type: ligand / ID: 4 / Number of copies: 1 / Formula: PAM
Molecular weightTheoretical: 254.408 Da
Chemical component information

ChemComp-PAM:
PALMITOLEIC ACID

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Macromolecule #5: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 5 / Number of copies: 2 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

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Macromolecule #6: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #7: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 7 / Number of copies: 1 / Formula: LPE
Molecular weightTheoretical: 510.708 Da
Chemical component information

ChemComp-LPE:
1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 10 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 8482332
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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