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Yorodumi- EMDB-6451: Unsharpened cryo-EM reconstruction of the GFP-E892-Vt-actin inter... -
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-Basic information
Entry | Database: EMDB / ID: EMD-6451 | |||||||||
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Title | Unsharpened cryo-EM reconstruction of the GFP-E892-Vt-actin interface for difference map calculation | |||||||||
Map data | Unsharpened reconstruction of N-terminal GFP fusion to VT residues 892-1061 bound to actin for difference map calculation | |||||||||
Sample |
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Keywords | actin / vinculin / cell migration / adhesion / mechanosensation / cytoskeleton | |||||||||
Function / homology | Function and homology information muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / epithelial cell-cell adhesion / zonula adherens ...muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / muscle alpha-actinin binding / MAP2K and MAPK activation / alpha-catenin binding / vinculin binding / fascia adherens / cell-cell contact zone / apical junction assembly / adherens junction assembly / costamere / regulation of establishment of endothelial barrier / alpha-actinin binding / axon extension / protein localization to cell surface / lamellipodium assembly / cytoskeletal motor activator activity / regulation of focal adhesion assembly / 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 / skeletal muscle fiber development / stress fiber / titin binding / regulation of cell migration / actin filament polymerization / filopodium / Neutrophil degranulation / 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 / neuromuscular junction / sarcolemma / Z disc / beta-catenin binding / actin filament binding / calcium-dependent protein binding / cell-cell junction / actin cytoskeleton / lamellipodium / cell body / scaffold protein binding / cytoskeleton / cell adhesion / mitochondrial inner membrane / cadherin binding / hydrolase activity / protein domain specific binding / focal adhesion / ubiquitin protein ligase binding / calcium ion binding / positive regulation of gene expression / structural molecule activity / magnesium ion binding / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Gallus gallus (chicken) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 16.4 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6451.map.gz | 4 MB | EMDB map data format | |
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Header (meta data) | emd-6451-v30.xml emd-6451.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
Images | emd_6451.png | 141 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6451 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6451 | HTTPS FTP |
-Validation report
Summary document | emd_6451_validation.pdf.gz | 79.6 KB | Display | EMDB validaton report |
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Full document | emd_6451_full_validation.pdf.gz | 78.6 KB | Display | |
Data in XML | emd_6451_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6451 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6451 | HTTPS FTP |
-Related structure data
Related structure data | 6446C 6447C 6448C 6449C 6450C 3jbiC 3jbjC 3jbkC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6451.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Unsharpened reconstruction of N-terminal GFP fusion to VT residues 892-1061 bound to actin for difference map calculation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : GFP-E892-Vt bound to F-actin
Entire | Name: GFP-E892-Vt bound to F-actin |
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Components |
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-Supramolecule #1000: GFP-E892-Vt bound to F-actin
Supramolecule | Name: GFP-E892-Vt bound to F-actin / type: sample / ID: 1000 Details: Helical filament with one vinculin tail domain bound per actin protomer Oligomeric state: One vinculin 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: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Muscle / Location in cell: Cytoplasm, cytoskeleton |
Molecular weight | Theoretical: 41.8 KDa |
Sequence | UniProtKB: Actin, alpha skeletal muscle |
-Macromolecule #2: Vinculin tail domain, residues 892-1061
Macromolecule | Name: Vinculin tail domain, residues 892-1061 / type: protein_or_peptide / ID: 2 / Name.synonym: GFP-E892-Vt / Details: N-terminal GFP fusion / Oligomeric state: helical / Recombinant expression: Yes |
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Source (natural) | Organism: Gallus gallus (chicken) / synonym: Chicken / Organelle: Focal adhesion / Location in cell: Cytoplasmic |
Molecular weight | Theoretical: 46 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: BL21(DE3) / Recombinant plasmid: H6-msfGFP (Addgene #29725) |
Sequence | UniProtKB: Vinculin |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.0125 mg/mL |
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Buffer | pH: 7 / Details: 50 mM KCl, 1 mM MgCl2, 1mM 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 GFP-E892-Vt was then applied and incubated for 60 ...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 GFP-E892-Vt was then applied and incubated for 60 seconds. 3 microliters of solution was removed, then an additional 3 microliters of GFP-E892-Vt 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 |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification. |
Date | Jul 9, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 212 / 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 | 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: 27.82 Å Applied symmetry - Helical parameters - Δ&Phi: 166.77 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.4 Å / Resolution method: OTHER / Software - Name: CTFFIND3, EMAN2/SPARX, FREALIGN |
CTF correction | Details: FREALIGN (per segment) |