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Yorodumi- EMDB-21925: Structural basis of alphaE-catenin - F-actin catch bond behavior -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21925 | |||||||||
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Title | Structural basis of alphaE-catenin - F-actin catch bond behavior | |||||||||
Map data | alphaE-catenin - F-actin catch bond behavior | |||||||||
Sample |
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Function / homology | Function and homology information negative regulation of integrin-mediated signaling pathway / VEGFR2 mediated vascular permeability / RHO GTPases activate IQGAPs / Adherens junctions interactions / gap junction assembly / epithelial cell-cell adhesion / zonula adherens / gamma-catenin binding / vinculin binding / cellular response to indole-3-methanol ...negative regulation of integrin-mediated signaling pathway / VEGFR2 mediated vascular permeability / RHO GTPases activate IQGAPs / Adherens junctions interactions / gap junction assembly / epithelial cell-cell adhesion / zonula adherens / gamma-catenin binding / vinculin binding / cellular response to indole-3-methanol / flotillin complex / negative regulation of cell motility / Myogenesis / apical junction assembly / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of smoothened signaling pathway / catenin complex / negative regulation of protein localization to nucleus / axon regeneration / cytoskeletal motor activator activity / negative regulation of neuroblast proliferation / smoothened signaling pathway / establishment or maintenance of cell polarity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / odontogenesis of dentin-containing tooth / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / neuroblast proliferation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / intercalated disc / skeletal muscle fiber development / stress fiber / ovarian follicle development / titin binding / extrinsic apoptotic signaling pathway in absence of ligand / actin filament polymerization / acrosomal vesicle / filopodium / actin filament / cell motility / integrin-mediated signaling pathway / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein localization / cell-cell adhesion / beta-catenin binding / response to estrogen / male gonad development / calcium-dependent protein binding / actin filament binding / cell-cell junction / cell migration / actin cytoskeleton / lamellipodium / cell junction / cell body / regulation of cell population proliferation / hydrolase activity / cadherin binding / protein domain specific binding / intracellular membrane-bounded organelle / apoptotic process / calcium ion binding / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / structural molecule activity / magnesium ion binding / ATP binding / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Mus musculus (house mouse) / Rabbit (rabbit) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.56 Å | |||||||||
Authors | Xu XP / Pokutta S / Torres M / Swift MF / Hanein D / Volkmann N / Weis WI | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Elife / Year: 2020 Title: Structural basis of αE-catenin-F-actin catch bond behavior. Authors: Xiao-Ping Xu / Sabine Pokutta / Megan Torres / Mark F Swift / Dorit Hanein / Niels Volkmann / William I Weis / Abstract: Cell-cell and cell-matrix junctions transmit mechanical forces during tissue morphogenesis and homeostasis. α-Catenin links cell-cell adhesion complexes to the actin cytoskeleton, and mechanical ...Cell-cell and cell-matrix junctions transmit mechanical forces during tissue morphogenesis and homeostasis. α-Catenin links cell-cell adhesion complexes to the actin cytoskeleton, and mechanical load strengthens its binding to F-actin in a direction-sensitive manner. Specifically, optical trap experiments revealed that force promotes a transition between weak and strong actin-bound states. Here, we describe the cryo-electron microscopy structure of the F-actin-bound αE-catenin actin-binding domain, which in solution forms a five-helix bundle. In the actin-bound structure, the first helix of the bundle dissociates and the remaining four helices and connecting loops rearrange to form the interface with actin. Deletion of the first helix produces strong actin binding in the absence of force, suggesting that the actin-bound structure corresponds to the strong state. Our analysis explains how mechanical force applied to αE-catenin or its homolog vinculin favors the strongly bound state, and the dependence of catch bond strength on the direction of applied force. | |||||||||
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_21925.map.gz | 6.1 MB | EMDB map data format | |
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Header (meta data) | emd-21925-v30.xml emd-21925.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
Images | emd_21925.png | 276.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21925 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21925 | HTTPS FTP |
-Related structure data
Related structure data | 6wvtMC M: atomic model generated by this map 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_21925.map.gz / Format: CCP4 / Size: 17.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | alphaE-catenin - F-actin catch bond behavior | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.035 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Complex of alphaE-catenin actin binding domain with F-actin
Entire | Name: Complex of alphaE-catenin actin binding domain with F-actin |
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Components |
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-Supramolecule #1: Complex of alphaE-catenin actin binding domain with F-actin
Supramolecule | Name: Complex of alphaE-catenin actin binding domain with F-actin type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: Actin, alpha skeletal muscle
Supramolecule | Name: Actin, alpha skeletal muscle / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
-Supramolecule #3: Catenin alpha-1
Supramolecule | Name: Catenin alpha-1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
-Macromolecule #1: Actin, alpha skeletal muscle
Macromolecule | Name: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Rabbit (rabbit) |
Molecular weight | Theoretical: 42.109973 KDa |
Sequence | String: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY ...String: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSS S LEKSYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQ KEITALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F |
-Macromolecule #2: Catenin alpha-1
Macromolecule | Name: Catenin alpha-1 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 25.999281 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: AIMAQLPQEQ KAKIAEQVAS FQEEKSKLDA EVSKWDDSGN DIIVLAKQMC MIMMEMTDFT RGKGPLKNTS DVISAAKKIA EAGSRMDKL GRTIADHCPD SACKQDLLAY LQRIALYCHQ LNICSKVKAE VQNLGGELVV SGVDSAMSLI QAAKNLMNAV V QTVKASYV ...String: AIMAQLPQEQ KAKIAEQVAS FQEEKSKLDA EVSKWDDSGN DIIVLAKQMC MIMMEMTDFT RGKGPLKNTS DVISAAKKIA EAGSRMDKL GRTIADHCPD SACKQDLLAY LQRIALYCHQ LNICSKVKAE VQNLGGELVV SGVDSAMSLI QAAKNLMNAV V QTVKASYV ASTKYQKSQG MASLNLPAVS WKMKAPEKKP LVKREKQDET QTKIKRASQK KHVNPVQALS EFKAMDSI |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 2-7 / Number grids imaged: 3 / Number real images: 5573 / Average exposure time: 1.0 sec. / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Segment selection | Number selected: 728331 |
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Startup model | Type of model: OTHER Details: in-house rabbit skeletal actin filament reconstruction filtered to 4 nm |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: RELION (ver. 3) |
Final reconstruction | Applied symmetry - Helical parameters - Δz: 27.4 Å Applied symmetry - Helical parameters - Δ&Phi: -166.9 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 422822 |