+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25883 | |||||||||
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Title | Full-length human E-cadherin bound to 19A11 activating Fab | |||||||||
Map data | cisTEM generate3D full map | |||||||||
Sample |
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Keywords | E-cadherin / Fab / CDH1 / functional antibody / CELL ADHESION | |||||||||
Function / homology | Function and homology information response to Gram-positive bacterium / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / pituitary gland development / gamma-catenin binding / desmosome / negative regulation of axon extension / cell-cell adhesion mediated by cadherin / cellular response to indole-3-methanol / flotillin complex / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules ...response to Gram-positive bacterium / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / pituitary gland development / gamma-catenin binding / desmosome / negative regulation of axon extension / cell-cell adhesion mediated by cadherin / cellular response to indole-3-methanol / flotillin complex / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Formation of definitive endoderm / catenin complex / Apoptotic cleavage of cell adhesion proteins / Adherens junctions interactions / GTPase activating protein binding / cell-cell junction assembly / adherens junction organization / apical junction complex / ankyrin binding / negative regulation of cell-cell adhesion / cellular response to lithium ion / homophilic cell adhesion via plasma membrane adhesion molecules / Transcriptional and post-translational regulation of MITF-M expression and activity / lateral plasma membrane / RHO GTPases activate IQGAPs / Integrin cell surface interactions / cell adhesion molecule binding / synapse assembly / Degradation of the extracellular matrix / InlA-mediated entry of Listeria monocytogenes into host cells / protein tyrosine kinase binding / negative regulation of cell migration / protein localization to plasma membrane / adherens junction / trans-Golgi network / cell morphogenesis / cell-cell adhesion / cytoplasmic side of plasma membrane / beta-catenin binding / positive regulation of protein import into nucleus / response to toxic substance / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / neuron projection development / actin cytoskeleton / cell migration / cell junction / lamellipodium / regulation of gene expression / postsynapse / endosome / cadherin binding / response to xenobiotic stimulus / glutamatergic synapse / calcium ion binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.83 Å | |||||||||
Authors | Maker A / Gumbiner BM | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Protein Expr Purif / Year: 2022 Title: Reconstitution of the full transmembrane cadherin-catenin complex. Authors: Allison Maker / Barry M Gumbiner / Abstract: The dynamic regulation of epithelial adherens junctions relies on all components of the E-cadherin-catenin complex. Previously, the complexes have been partially reconstituted and composed only of α- ...The dynamic regulation of epithelial adherens junctions relies on all components of the E-cadherin-catenin complex. Previously, the complexes have been partially reconstituted and composed only of α-catenin, β-catenin, and the E-cadherin cytoplasmic domain. However, p120-catenin and the full-length E-cadherin including the extracellular, transmembrane, and intra-cellular domains are vital to the understanding of the relationship between extracellular adhesion and intracellular signaling. Here, we reconstitute the complete and full-length cadherin-catenin complex, including full-length E-cadherin, α-catenin, β-catenin, and p120-catenin, into nanodiscs. We are able to observe the cadherin in nanodiscs by cryo-EM. We also reconstitute α-catenin, β-catenin, and p120-catenin with the E-cadherin cytoplasmic tail alone in order to analyze the affinities of their binding interactions. We find that p120-catenin does not associate strongly with α- or β-catenin and binds much more transiently to the cadherin cytoplasmic tail than does β-catenin. Overall, this work creates many new possibilities for biochemical studies understanding transmembrane signaling of cadherins and the role of p120-catenin in adhesion activation. | |||||||||
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_25883.map.gz | 226.1 MB | EMDB map data format | |
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Header (meta data) | emd-25883-v30.xml emd-25883.xml | 19.7 KB 19.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25883_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_25883.png | 39 KB | ||
Filedesc metadata | emd-25883.cif.gz | 5.8 KB | ||
Others | emd_25883_half_map_1.map.gz emd_25883_half_map_2.map.gz | 185.2 MB 185.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25883 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25883 | HTTPS FTP |
-Validation report
Summary document | emd_25883_validation.pdf.gz | 1003 KB | Display | EMDB validaton report |
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Full document | emd_25883_full_validation.pdf.gz | 1002.6 KB | Display | |
Data in XML | emd_25883_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | emd_25883_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25883 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25883 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25883.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | cisTEM generate3D full map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: cisTEM generate3D half-map 1
File | emd_25883_half_map_1.map | ||||||||||||
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Annotation | cisTEM generate3D half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cisTEM generate3D half-map 2
File | emd_25883_half_map_2.map | ||||||||||||
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Annotation | cisTEM generate3D half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of human E-cadherin monomer with activating Fab 19A11
Entire | Name: Complex of human E-cadherin monomer with activating Fab 19A11 |
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Components |
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-Supramolecule #1: Complex of human E-cadherin monomer with activating Fab 19A11
Supramolecule | Name: Complex of human E-cadherin monomer with activating Fab 19A11 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Cadherin was embedded in MSP1D1 nanodisc not visible in final map. Alpha-catenin, beta-catenin, p120-catenin also present in EM sample, but were not visible in any images. |
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Molecular weight | Theoretical: 130 KDa |
-Supramolecule #2: Full length E-cadherin with Twin-Strep tag
Supramolecule | Name: Full length E-cadherin with Twin-Strep tag / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 80 KDa |
-Supramolecule #3: Activating antibody fragment 19A11
Supramolecule | Name: Activating antibody fragment 19A11 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 / Details: His tagged recombinant Fab fragment |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 50 KDa |
-Macromolecule #1: E-cadherin (CDH1) with C-terminal Twin-Strep tag
Macromolecule | Name: E-cadherin (CDH1) with C-terminal Twin-Strep tag / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DWVIPPISCP ENEKGPFPKN LVQIKSNKDK EGKVFYSITG QGADTPPVGV FIIERETGWL KVTEPLDRER IATYTLFSHA VSSNGNAVED PMEILITVTD QNDNKPEFTQ EVFKGSVMEG ALPGTSVMEV TATDADDDVN TYNAAIAYTI LSQDPELPDK NMFTINRNTG ...String: DWVIPPISCP ENEKGPFPKN LVQIKSNKDK EGKVFYSITG QGADTPPVGV FIIERETGWL KVTEPLDRER IATYTLFSHA VSSNGNAVED PMEILITVTD QNDNKPEFTQ EVFKGSVMEG ALPGTSVMEV TATDADDDVN TYNAAIAYTI LSQDPELPDK NMFTINRNTG VISVVTTGLD RESFPTYTLV VQAADLQGEG LSTTATAVIT VTDTNDNPPI FNPTTYKGQV PENEANVVIT TLKVTDADAP NTPAWEAVYT ILNDDGGQFV VTTNPVNNDG ILKTAKGLDF EAKQQYILHV AVTNVVPFEV SLTTSTATVT VDVLDVNEAP IFVPPEKRVE VSEDFGVGQE ITSYTAQEPD TFMEQKITYR IWRDTANWLE INPDTGAIST RAELDREDFE HVKNSTYTAL IIATDNGSPV ATGTGTLLLI LSDVNDNAPI PEPRTIFFCE RNPKPQVINI IDADLPPNTS PFTAELTHGA SANWTIQYND PTQESIILKP KMALEVGDYK INLKLMDNQN KDQVTTLEVS VCDCEGAAGV CRKAQPVEAG LQIPAILGIL GGILALLILI LLLLLFLRRR AVVKEPLLPP EDDTRDNVYY YDEEGGGEED QDFDLSQLHR GLDARPEVTR NDVAPTLMSV PRYLPRPANP DEIGNFIDEN LKAADTDPTA PPYDSLLVFD YEGSGSEAAS LSSLNSSESD KDQDYDYLNE WGNRFKKLAD MYGGGEDHSA WSHPQFEKGG GSGGGSGGSA WSHPQFEK |
-Macromolecule #2: Activating antibody fragment 19A11 heavy chain
Macromolecule | Name: Activating antibody fragment 19A11 heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: QVQLKESGPG LVAPSQSLSI TCTVSGFSLS RYGVHWVRQP PGKGLEWLGM MWGGGNTDYN SALKSRLSIS KDNSKSQVFL KMNSLQTDDT AMYYCASSNY VLGYAMDYWG QGTSVTVSSA KTTPPSVYPL APGSAAQTNS MVTLGCLVKG YFPEPVTVTW NSGSLSSGVH ...String: QVQLKESGPG LVAPSQSLSI TCTVSGFSLS RYGVHWVRQP PGKGLEWLGM MWGGGNTDYN SALKSRLSIS KDNSKSQVFL KMNSLQTDDT AMYYCASSNY VLGYAMDYWG QGTSVTVSSA KTTPPSVYPL APGSAAQTNS MVTLGCLVKG YFPEPVTVTW NSGSLSSGVH TFPAVLQSDL YTLSSSVTVP SSPRPSETVT CNVAHPASST KVDKKIVPRD CHHHHHH |
-Macromolecule #3: Activating antibody fragment 19A11 light chain
Macromolecule | Name: Activating antibody fragment 19A11 light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: DIVMTQSPSS LAMSVGQKVT MNCKSSQSLL NSSNQKNYLA WYQQKPGQSP KLLIYFTSTR GSGVPDRFIG SGSGTDFTLT ISSVEAEDLA DYFCQQHYRT PHTFGGGTKV EIKRADAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE RQNGVLNSWT ...String: DIVMTQSPSS LAMSVGQKVT MNCKSSQSLL NSSNQKNYLA WYQQKPGQSP KLLIYFTSTR GSGVPDRFIG SGSGTDFTLT ISSVEAEDLA DYFCQQHYRT PHTFGGGTKV EIKRADAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE RQNGVLNSWT DQDSKDSTYS MSSTLTLTKD EYERHNSYTC EATHKTSTSP IVKSFNRNEC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.10 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | Alpha-catenin, beta-catenin, p120 catenin also present at sample prep stage. These were not visible on grid. Nanodiscs averaged out in final reconstruction. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |