+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25884 | |||||||||
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Title | Full-length human E-cadherin bound to neutral Fab 46H7 | |||||||||
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 / negative regulation of axon extension / cell-cell adhesion mediated by cadherin / cellular response to indole-3-methanol / flotillin complex / Formation of definitive endoderm / 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 / negative regulation of axon extension / cell-cell adhesion mediated by cadherin / cellular response to indole-3-methanol / flotillin complex / Formation of definitive endoderm / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Adherens junctions interactions / catenin complex / Apoptotic cleavage of cell adhesion proteins / 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 / lateral plasma membrane / RHO GTPases activate IQGAPs / Integrin cell surface interactions / cell adhesion molecule binding / synapse assembly / InlA-mediated entry of Listeria monocytogenes into host cells / Degradation of the extracellular matrix / negative regulation of cell migration / protein tyrosine kinase binding / protein localization to plasma membrane / adherens junction / cell morphogenesis / trans-Golgi network / cytoplasmic side of plasma membrane / response to toxic substance / beta-catenin binding / cell-cell adhesion / positive regulation of protein import into nucleus / neuron projection development / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / actin cytoskeleton / lamellipodium / cell junction / postsynapse / regulation of gene expression / endosome / response to xenobiotic stimulus / cadherin binding / glutamatergic synapse / calcium ion binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / 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: 4.56 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_25884.map.gz | 226.2 MB | EMDB map data format | |
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Header (meta data) | emd-25884-v30.xml emd-25884.xml | 19.8 KB 19.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25884_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_25884.png | 38.1 KB | ||
Filedesc metadata | emd-25884.cif.gz | 5.8 KB | ||
Others | emd_25884_half_map_1.map.gz emd_25884_half_map_2.map.gz | 185.2 MB 185.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25884 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25884 | HTTPS FTP |
-Validation report
Summary document | emd_25884_validation.pdf.gz | 1023.5 KB | Display | EMDB validaton report |
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Full document | emd_25884_full_validation.pdf.gz | 1023.1 KB | Display | |
Data in XML | emd_25884_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | emd_25884_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25884 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25884 | 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_25884.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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 2
File | emd_25884_half_map_1.map | ||||||||||||
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Annotation | cisTEM generate3D half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cisTEM generate3D half map 1
File | emd_25884_half_map_2.map | ||||||||||||
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Annotation | cisTEM generate3D half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of human E-cadherin monomer with neutral Fab 46H7
Entire | Name: Complex of human E-cadherin monomer with neutral Fab 46H7 |
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Components |
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-Supramolecule #1: Complex of human E-cadherin monomer with neutral Fab 46H7
Supramolecule | Name: Complex of human E-cadherin monomer with neutral Fab 46H7 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: Neutral antibody fragment 46H7 Fab
Supramolecule | Name: Neutral antibody fragment 46H7 Fab / 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: Neutral antibody fragment 46H7 heavy chain
Macromolecule | Name: Neutral antibody fragment 46H7 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: MGWSCIILFL VATATGVHSQ VQLQQSGAEL VRPGASVKIS CKAFGYTFTN HHINWVKQRP GQGLDWIGYI YPYNDYTSYN QKFEGKATLT VDKSSSTAYM ELSSLTSEDS AVYYCARGGG YDWFAYWGQG TLVTVSAAKT TPPSVYPLAP GSAAQTNSMV TLGCLVKGYF ...String: MGWSCIILFL VATATGVHSQ VQLQQSGAEL VRPGASVKIS CKAFGYTFTN HHINWVKQRP GQGLDWIGYI YPYNDYTSYN QKFEGKATLT VDKSSSTAYM ELSSLTSEDS AVYYCARGGG YDWFAYWGQG TLVTVSAAKT TPPSVYPLAP GSAAQTNSMV TLGCLVKGYF PEPVTVTWNS GSLSSGVHTF PAVLQSDLYT LSSSVTVPSS PRPSETVTCN VAHPASSTKV DKKIVPRDCH HHHHH |
-Macromolecule #3: Neutral antibody fragment 46H7 light chain
Macromolecule | Name: Neutral antibody fragment 46H7 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: MGWSCIILFL VATATGVHSD IQMTQSPASL SVSVGETVTI TCRASENIYS NLAWYQQKQG KSPQLLVYAA TNLADGVPSR FSGSGSGTQY SLKINSLQSE DFGNYYCQHF WGTPYKFGGG TKLEIKRADA APTVSIFPPS SEQLTSGGAS VVCFLNNFYP KDINVKWKID ...String: MGWSCIILFL VATATGVHSD IQMTQSPASL SVSVGETVTI TCRASENIYS NLAWYQQKQG KSPQLLVYAA TNLADGVPSR FSGSGSGTQY SLKINSLQSE DFGNYYCQHF WGTPYKFGGG TKLEIKRADA APTVSIFPPS SEQLTSGGAS VVCFLNNFYP KDINVKWKID GSERQNGVLN SWTDQDSKDS TYSMSSTLTL TKDEYERHNS YTCEATHKTS TSPIVKSFNR NEC |
-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 | ||||||||||||
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) / Detector mode: SUPER-RESOLUTION / 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: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |