+Open data
-Basic information
Entry | Database: PDB / ID: 3jbi | ||||||
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Title | MDFF model of the vinculin tail domain bound to F-actin | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / cytoskeleton / adhesion | ||||||
Function / homology | Function and homology information muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / epithelial cell-cell adhesion / zonula adherens ...muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / epithelial cell-cell adhesion / zonula adherens / muscle alpha-actinin binding / dystroglycan binding / MAP2K and MAPK activation / alpha-catenin binding / vinculin binding / fascia adherens / cell-cell contact zone / apical junction assembly / costamere / regulation of establishment of endothelial barrier / adherens junction assembly / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / alpha-actinin binding / filamentous actin / actin filament bundle / brush border / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / regulation of cell migration / actin filament polymerization / filopodium / cell projection / Neutrophil degranulation / actin filament / morphogenesis of an epithelium / 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 / calcium-dependent protein binding / cell-cell junction / actin filament binding / actin cytoskeleton / lamellipodium / cell body / scaffold protein binding / mitochondrial inner membrane / cytoskeleton / cell adhesion / hydrolase activity / cadherin binding / 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 | Gallus gallus (chicken) Oryctolagus cuniculus (rabbit) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 8.5 Å | ||||||
Authors | Kim, L.Y. / Thompson, P.M. / Lee, H.T. / Pershad, M. / Campbell, S.L. / Alushin, G.M. | ||||||
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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3jbi.cif.gz | 163 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jbi.ent.gz | 122.1 KB | Display | PDB format |
PDBx/mmJSON format | 3jbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jbi_validation.pdf.gz | 877.7 KB | Display | wwPDB validaton report |
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Full document | 3jbi_full_validation.pdf.gz | 888.7 KB | Display | |
Data in XML | 3jbi_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 3jbi_validation.cif.gz | 43.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/3jbi ftp://data.pdbj.org/pub/pdb/validation_reports/jb/3jbi | HTTPS FTP |
-Related structure data
Related structure data | 6446MC 6447C 6448C 6449C 6450C 6451C 3jbjC 3jbkC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-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: -166.82 °) |
-Components
#1: Protein | Mass: 41862.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle / References: UniProt: P68135 #2: Protein | | Mass: 28241.018 Da / Num. of mol.: 1 / Fragment: tail domain (UNP residues 879-1130) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: VCL, VINC1 / Organelle: focal adhesion / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12003 #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 |
-Sample preparation
Component |
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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 Vt was then applied and incubated for 60 seconds. 3 ...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 Vt was then applied and incubated for 60 seconds. 3 microliters of solution was removed, then an additional 3 microliters of Vt 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 Vt 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 Vt was then applied and incubated for 60 seconds. 3 microliters of solution was removed, then an additional 3 microliters of Vt applied. After 60 seconds, 3 microliters of solution was removed, then the grid was blotted for 2 seconds before plunging. |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: May 22, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM |
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: 1384 |
-Processing
EM software |
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CTF correction | Details: FREALIGN (per segment) | ||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 166.82 ° / Axial rise/subunit: 27.8 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||
3D reconstruction | Method: IHRSR / Resolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Nominal pixel size: 2.18 Å / Actual pixel size: 2.18 Å / Magnification calibration: catalase crystal Details: (Helical Details: Single model IHRSR was performed 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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