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Open data
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Basic information
Entry | Database: PDB / ID: 3jbk | ||||||
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Title | Cryo-EM reconstruction of the metavinculin-actin interface | ||||||
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![]() | STRUCTURAL PROTEIN / actin / metavinculin / vinculin / cell migration / adhesion / mechanosensation / cytoskeleton | ||||||
Function / homology | ![]() regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding ...regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / adherens junction assembly / apical junction assembly / costamere / regulation of establishment of endothelial barrier / axon extension / protein localization to cell surface / lamellipodium assembly / cytoskeletal motor activator activity / regulation of focal adhesion assembly / maintenance of blood-brain barrier / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / brush border / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / Smooth Muscle Contraction / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / negative regulation of cell migration / cell-matrix adhesion / filopodium / cell projection / morphogenesis of an epithelium / actin filament / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / sarcolemma / beta-catenin binding / platelet aggregation / specific granule lumen / 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 / calcium-dependent protein binding / Signaling by BRAF and RAF1 fusions / cell-cell junction / extracellular vesicle / Signaling by ALK fusions and activated point mutants / Platelet degranulation / lamellipodium / actin binding / cell body / secretory granule lumen / ficolin-1-rich granule lumen / molecular adaptor activity / cytoskeleton / hydrolase activity / cell adhesion / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 8.2 Å | ||||||
![]() | Kim, L.Y. / Thompson, P.M. / Lee, H.T. / Pershad, M. / Campbell, S.L. / Alushin, G.M. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.3 KB | Display | ![]() |
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PDB format | ![]() | 121.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 889.6 KB | Display | ![]() |
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Full document | ![]() | 898.2 KB | Display | |
Data in XML | ![]() | 29.7 KB | Display | |
Data in CIF | ![]() | 43.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6447MC ![]() 6446C ![]() 6448C ![]() 6449C ![]() 6450C ![]() 6451C ![]() 3jbiC ![]() 3jbjC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 1 / Rise per n subunits: 27.8 Å / Rotation per n subunits: -166.75 °) |
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Components
#1: Protein | Mass: 41862.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | | Mass: 29878.275 Da / Num. of mol.: 1 / Fragment: tail domain (UNP residues 858-1129) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
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Sample preparation
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Buffer solution | Name: 50 mM KCl, 1 mM MgCl2, 1 mM EGTA, 10 mM imidazole / pH: 7 / Details: 50 mM KCl, 1 mM MgCl2, 1 mM EGTA, 10 mM imidazole | ||||||||||||||||||||
Specimen | Conc.: 0.0125 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Details: 200 mesh 1.2 / 1.3 C-flat | ||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % Details: 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. ...Details: 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 into liquid ethane (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 imaging
Microscopy | Model: FEI TECNAI 20 / Date: Oct 10, 2014 |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 100000 X / Calibrated magnification: 137615 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2 mm Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification. |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Image scans | Num. digital images: 671 |
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Processing
EM software |
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CTF correction | Details: FREALIGN (per segment) | ||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 166.75 ° / Axial rise/subunit: 27.8 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||
3D reconstruction | Method: IHRSR / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Nominal pixel size: 2.18 Å / Actual pixel size: 2.18 Å Details: (Helical 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 ...Details: (Helical 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).) Symmetry type: HELICAL | ||||||||||||||||||||||||||||
Atomic model building |
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Atomic model building | Pdb chain-ID: A / Source name: PDB / Type: experimental model
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Refinement step | Cycle: LAST
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