+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6448 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM reconstruction of F-actin | |||||||||
Map data | Control reconstruction of F-actin alone | |||||||||
Sample |
| |||||||||
Keywords | actin / cell migration / adhesion / mechanosensation / cytoskeleton | |||||||||
Function / homology | Function and homology information cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly ...cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 7.6 Å | |||||||||
Authors | Kim LY / Thompson PM / Lee HT / Pershad M / Campbell SL / Alushin GM | |||||||||
Citation | Journal: J Mol Biol / Year: 2016 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 |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6448.map.gz | 25.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6448-v30.xml emd-6448.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
Images | emd_6448.png | 168 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6448 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6448 | 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 (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_6448.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Control reconstruction of F-actin alone | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : F-actin
Entire | Name: F-actin |
---|---|
Components |
|
-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 |
---|
-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: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Muscle / Location in cell: Cytoplasm, cytoskeleton |
Molecular weight | Theoretical: 41.8 KDa |
Sequence | UniProtKB: Actin, alpha skeletal muscle |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | 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. The grid was blotted for 2 seconds before plunging. |
-Electron microscopy
Microscope | FEI TECNAI 20 |
---|---|
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 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
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 |
-Image processing
Details | Single-model IHRSR was performed with EMAN2 / SPARX and final reconstruction with FREALIGN (fixed helical parameters). |
---|---|
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 |
CTF correction | Details: FREALIGN (per segment) |