+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22806 | |||||||||
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Title | Human WLS in complex with WNT8A | |||||||||
Map data | Density modified map | |||||||||
Sample |
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Function / homology | Function and homology information : / : / Wnt protein secretion / neural crest cell fate commitment / positive regulation of Wnt protein secretion / WNT ligand biogenesis and trafficking / secondary palate development / cementum mineralization / beta-catenin destruction complex disassembly / hindbrain development ...: / : / Wnt protein secretion / neural crest cell fate commitment / positive regulation of Wnt protein secretion / WNT ligand biogenesis and trafficking / secondary palate development / cementum mineralization / beta-catenin destruction complex disassembly / hindbrain development / Wnt-protein binding / exocrine pancreas development / frizzled binding / Class B/2 (Secretin family receptors) / Disassembly of the destruction complex and recruitment of AXIN to the membrane / anterior/posterior axis specification / midbrain development / organelle membrane / cell fate commitment / mesoderm formation / positive regulation of Wnt signaling pathway / canonical Wnt signaling pathway / endomembrane system / response to retinoic acid / TCF dependent signaling in response to WNT / cytokine activity / intracellular protein transport / trans-Golgi network / neuron differentiation / Wnt signaling pathway / positive regulation of canonical Wnt signaling pathway / endocytic vesicle membrane / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / cytoplasmic vesicle / collagen-containing extracellular matrix / early endosome / receptor ligand activity / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.19 Å | |||||||||
Authors | Nygaard R / Jia Y / Kim J / Ross D / Parisi G / Clarke OB / Virshup DM / Mancia F | |||||||||
Funding support | United States, Singapore, 2 items
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Citation | Journal: Cell / Year: 2021 Title: Structural Basis of WLS/Evi-Mediated Wnt Transport and Secretion. Authors: Rie Nygaard / Jia Yu / Jonathan Kim / Daniel R Ross / Giacomo Parisi / Oliver B Clarke / David M Virshup / Filippo Mancia / Abstract: Wnts are evolutionarily conserved ligands that signal at short range to regulate morphogenesis, cell fate, and stem cell renewal. The first and essential steps in Wnt secretion are their O- ...Wnts are evolutionarily conserved ligands that signal at short range to regulate morphogenesis, cell fate, and stem cell renewal. The first and essential steps in Wnt secretion are their O-palmitoleation and subsequent loading onto the dedicated transporter Wntless/evenness interrupted (WLS/Evi). We report the 3.2 Å resolution cryogenic electron microscopy (cryo-EM) structure of palmitoleated human WNT8A in complex with WLS. This is accompanied by biochemical experiments to probe the physiological implications of the observed association. The WLS membrane domain has close structural homology to G protein-coupled receptors (GPCRs). A Wnt hairpin inserts into a conserved hydrophobic cavity in the GPCR-like domain, and the palmitoleate protrudes between two helices into the bilayer. A conformational switch of highly conserved residues on a separate Wnt hairpin might contribute to its transfer to receiving cells. This work provides molecular-level insights into a central mechanism in animal body plan development and stem cell biology. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22806.map.gz | 9.2 MB | EMDB map data format | |
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Header (meta data) | emd-22806-v30.xml emd-22806.xml | 21.6 KB 21.6 KB | Display Display | EMDB header |
Images | emd_22806.png | 86.7 KB | ||
Masks | emd_22806_msk_1.map emd_22806_msk_2.map | 347.6 MB 347.6 MB | Mask map | |
Others | emd_22806_additional_1.map.gz emd_22806_half_map_1.map.gz emd_22806_half_map_2.map.gz | 9.1 MB 322.2 MB 322.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22806 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22806 | HTTPS FTP |
-Validation report
Summary document | emd_22806_validation.pdf.gz | 958.6 KB | Display | EMDB validaton report |
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Full document | emd_22806_full_validation.pdf.gz | 958.2 KB | Display | |
Data in XML | emd_22806_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | emd_22806_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22806 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22806 | HTTPS FTP |
-Related structure data
Related structure data | 7kc4MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10699 (Title: Human WLS in complex with WNT8A / Data size: 1.9 TB Data #1: Unaligned multi frame micrographs of WNT8A WLS complex [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22806.map.gz / Format: CCP4 / Size: 9.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Density modified map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_22806_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_22806_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Blurred map (B=100)
File | emd_22806_additional_1.map | ||||||||||||
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Annotation | Blurred map (B=100) | ||||||||||||
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Density Histograms |
-Half map: Half map
File | emd_22806_half_map_1.map | ||||||||||||
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Annotation | Half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map
File | emd_22806_half_map_2.map | ||||||||||||
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Annotation | Half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of WLS/Evi and WNT8A in nanodisc
Entire | Name: Complex of WLS/Evi and WNT8A in nanodisc |
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Components |
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-Supramolecule #1: Complex of WLS/Evi and WNT8A in nanodisc
Supramolecule | Name: Complex of WLS/Evi and WNT8A in nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Nanodisc were formed using MSP1E3D1 and POPG lipid |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: FreeStyle 293-F Cells |
Molecular weight | Theoretical: 105.6 KDa |
-Macromolecule #1: Protein Wnt-8a
Macromolecule | Name: Protein Wnt-8a / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 40.052359 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGNLFMLWAA LGICCAAFSA SAWSVNNFLI TGPKAYLTYT TSVALGAQSG IEECKFQFAW ERWNCPENAL QLSTHNRLRS ATRETSFIH AISSAGVMYI ITKNCSMGDF ENCGCDGSNN GKTGGHGWIW GGCSDNVEFG ERISKLFVDS LEKGKDARAL M NLHNNRAG ...String: MGNLFMLWAA LGICCAAFSA SAWSVNNFLI TGPKAYLTYT TSVALGAQSG IEECKFQFAW ERWNCPENAL QLSTHNRLRS ATRETSFIH AISSAGVMYI ITKNCSMGDF ENCGCDGSNN GKTGGHGWIW GGCSDNVEFG ERISKLFVDS LEKGKDARAL M NLHNNRAG RLAVRATMKR TCKCHGISGS CSIQTCWLQL AEFREMGDYL KAKYDQALKI EMDKRQLRAG NSAEGHWVPA EA FLPSAEA ELIFLEESPD YCTCNSSLGI YGTEGRECLQ NSHNTSRWER RSCGRLCTEC GLQVEERKTE VISSCNCKFQ WCC TVKCDQ CRHVVSKYYC ARSPGSAQSL GKGSAGGWSH PQFEK |
-Macromolecule #2: Protein wntless homolog
Macromolecule | Name: Protein wntless homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 65.64943 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 TRKEAQEAEN LYFQSHHHHH HHHHHD YKD DDDK |
-Macromolecule #5: PALMITIC ACID
Macromolecule | Name: PALMITIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: PLM |
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Molecular weight | Theoretical: 256.424 Da |
Chemical component information | ChemComp-PLM: |
-Macromolecule #6: 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL
Macromolecule | Name: 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL type: ligand / ID: 6 / Number of copies: 3 / Formula: DR9 |
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Molecular weight | Theoretical: 746.991 Da |
Chemical component information | ChemComp-DR9: |
-Macromolecule #7: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: Y01 |
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Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ChemComp-Y01: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | |||||||||
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Buffer | pH: 8 / Component:
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Grid | Model: Quantifoil R0.6/1 / Material: GOLD / Pretreatment - Type: PLASMA CLEANING | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 1 / Number real images: 12747 / Average exposure time: 3.0 sec. / Average electron dose: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |