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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6447 | |||||||||
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Title | Cryo-EM reconstruction of the metavinculin-actin interface | |||||||||
![]() | Reconstruction of metavinculin tail domain bound to F-actin | |||||||||
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![]() | actin / metavinculin / vinculin / cell migration / adhesion / mechanosensation / cytoskeleton | |||||||||
Function / homology | ![]() regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding ...regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / apical junction assembly / costamere / regulation of establishment of endothelial barrier / adherens junction assembly / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / cytoskeletal motor activator activity / maintenance of blood-brain barrier / tropomyosin binding / myosin heavy chain binding / troponin I binding / mesenchyme migration / filamentous actin / actin filament bundle / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / brush border / striated muscle thin filament / actin filament bundle assembly / skeletal muscle thin filament assembly / skeletal muscle myofibril / actin monomer binding / Smooth Muscle Contraction / stress fiber / skeletal muscle fiber development / titin binding / actin filament polymerization / negative regulation of cell migration / cell-matrix adhesion / filopodium / cell projection / morphogenesis of an epithelium / actin filament / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / sarcolemma / beta-catenin binding / platelet aggregation / specific granule lumen / calcium-dependent protein binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / cell-cell junction / extracellular vesicle / Platelet degranulation / lamellipodium / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / actin binding / cell body / secretory granule lumen / molecular adaptor activity / ficolin-1-rich granule lumen / cytoskeleton / cell adhesion / hydrolase activity / cadherin binding / membrane raft / protein domain specific binding / focal adhesion / ubiquitin protein ligase binding / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / structural molecule activity / magnesium ion binding / protein-containing complex / extracellular exosome / extracellular region / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 8.2 Å | |||||||||
![]() | Kim LY / Thompson PM / Lee HT / Pershad M / Campbell SL / Alushin GM | |||||||||
![]() | ![]() Title: The Structural Basis of Actin Organization by Vinculin and Metavinculin. Authors: Laura Y Kim / Peter M Thompson / Hyunna T Lee / Mihir Pershad / Sharon L Campbell / Gregory M Alushin / ![]() Abstract: Vinculin is an essential adhesion protein that links membrane-bound integrin and cadherin receptors through their intracellular binding partners to filamentous actin, facilitating mechanotransduction. ...Vinculin is an essential adhesion protein that links membrane-bound integrin and cadherin receptors through their intracellular binding partners to filamentous actin, facilitating mechanotransduction. Here we present an 8.5-Å-resolution cryo-electron microscopy reconstruction and pseudo-atomic model of the vinculin tail (Vt) domain bound to F-actin. Upon actin engagement, the N-terminal "strap" and helix 1 are displaced from the Vt helical bundle to mediate actin bundling. We find that an analogous conformational change also occurs in the H1' helix of the tail domain of metavinculin (MVt) upon actin binding, a muscle-specific splice isoform that suppresses actin bundling by Vt. These data support a model in which metavinculin tunes the actin bundling activity of vinculin in a tissue-specific manner, providing a mechanistic framework for understanding metavinculin mutations associated with hereditary cardiomyopathies. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 25.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.2 KB 13.2 KB | Display Display | ![]() |
Images | ![]() | 209.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 318.4 KB | Display | ![]() |
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Full document | ![]() | 318 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jbkMC ![]() 6446C ![]() 6448C ![]() 6449C ![]() 6450C ![]() 6451C ![]() 3jbiC ![]() 3jbjC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Reconstruction of metavinculin tail domain bound to F-actin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Metavinculin tail domain bound to F-actin
Entire | Name: Metavinculin tail domain bound to F-actin |
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Components |
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-Supramolecule #1000: Metavinculin tail domain bound to F-actin
Supramolecule | Name: Metavinculin tail domain bound to F-actin / type: sample / ID: 1000 Details: Helical filament with one metavinculin tail domain bound per actin protomer Oligomeric state: One metavinculin tail domain per actin protomer Number unique components: 2 |
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-Macromolecule #1: skeletal muscle actin
Macromolecule | Name: skeletal muscle actin / type: protein_or_peptide / ID: 1 / Name.synonym: actin / Oligomeric state: helical filament / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 41.8 KDa |
Sequence | UniProtKB: Actin, alpha skeletal muscle |
-Macromolecule #2: Metavinculin tail domain, residues 858-1129
Macromolecule | Name: Metavinculin tail domain, residues 858-1129 / type: protein_or_peptide / ID: 2 / Name.synonym: MVt / Oligomeric state: helical / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 29.6 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: Vinculin |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Concentration | 0.0125 mg/mL |
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Buffer | pH: 7 / Details: 50 mM KCl, 1 mM MgCl2, 1 mM EGTA, 10 mM imidazole |
Grid | Details: 200 mesh 1.2 / 1.3 C-flat |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: LEICA EM GP Method: 3 microliters of 0.3 micromolar actin was applied to the grid and incubated for 60 seconds at 25 degrees C. 3 microliters of 10 micromolar MVt was then applied and incubated for 60 seconds. 3 ...Method: 3 microliters of 0.3 micromolar actin was applied to the grid and incubated for 60 seconds at 25 degrees C. 3 microliters of 10 micromolar MVt was then applied and incubated for 60 seconds. 3 microliters of solution was removed, then an additional 3 microliters of MVt applied. After 60 seconds, 3 microliters of solution was removed, then the grid was blotted for 2 seconds before plunging. |
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Electron microscopy
Microscope | FEI TECNAI 20 |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification. |
Date | Sep 10, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 671 / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 137615 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 100000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
Details | Multi-model IHRSR was performed using EMAN2 / SPARX to select for bound segments, followed by single-model IHRSR with EMAN2 / SPARX and final reconstruction with FREALIGN (fixed helical parameters). |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 27.80 Å Applied symmetry - Helical parameters - Δ&Phi: 166.75 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: OTHER / Software - Name: CTFFIND3, EMAN2/SPARX, FREALIGN |
CTF correction | Details: FREALIGN (per segment) |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera, MDFF |
Details | Components were initially rigid body fit using Chimera, followed by flexible fitting with MDFF. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-3jbk: |