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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6448 | |||||||||
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Title | Cryo-EM reconstruction of F-actin | |||||||||
![]() | Control reconstruction of F-actin alone | |||||||||
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Function / homology | ![]() cytoskeletal motor activator activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | helical reconstruction / ![]() | |||||||||
![]() | 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
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 25.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.7 KB 10.7 KB | Display Display | ![]() |
Images | ![]() | 168 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jbjMC ![]() 6446C ![]() 6447C ![]() 6449C ![]() 6450C ![]() 6451C ![]() 3jbiC ![]() 3jbkC 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 | Control reconstruction of F-actin alone | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : F-actin
Entire | Name: F-actin![]() |
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Components |
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-Supramolecule #1000: F-actin
Supramolecule | Name: F-actin / type: sample / ID: 1000 / Details: Helical filament of F-actin / Oligomeric state: Helical / Number unique components: 1 |
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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: ![]() |
-Experimental details
-Structure determination
Method | ![]() |
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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. The grid was blotted for 2 seconds before plunging. |
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Electron microscopy
Microscope | FEI TECNAI 20 |
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Electron beam | Acceleration voltage: 120 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 137615 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification. |
Date | May 13, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 1257 / Average electron dose: 25 e/Å2 |
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Image processing
CTF correction | Details: FREALIGN (per segment) |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 27.80 Å Applied symmetry - Helical parameters - Δ&Phi: 166.67 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: OTHER / Software - Name: CTFFIND3, EMAN2/SPARX, FREALIGN |
Details | Single-model IHRSR was performed with EMAN2 / SPARX and final reconstruction with FREALIGN (fixed helical parameters). |