+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-6447 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM reconstruction of the metavinculin-actin interface | |||||||||
![]() | Reconstruction of metavinculin tail domain bound to F-actin | |||||||||
![]() |
| |||||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 25.6 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 13.2 KB 13.2 KB | Display Display | ![]() |
Images | ![]() | 209.2 KB | ||
Archive 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 ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction of metavinculin tail domain bound to F-actin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : Metavinculin tail domain bound to F-actin
Entire | Name: Metavinculin tail domain bound to F-actin |
---|---|
Components |
|
-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 |
---|
-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 |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 41.8 KDa |
Sequence | UniProtKB: ![]() |
-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 |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 29.6 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | UniProtKB: ![]() |
-Experimental details
-Structure determination
Method | ![]() |
---|---|
![]() | helical reconstruction |
Aggregation state | filament |
-
Sample preparation
Concentration | 0.0125 mg/mL |
---|---|
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. |
-
Electron microscopy
Microscope | FEI TECNAI 20 |
---|---|
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 | 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 |
-
Image processing
CTF correction | Details: FREALIGN (per segment) |
---|---|
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 |
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). |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
---|---|
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: |