+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6124 | |||||||||
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Title | Structure of the F-actin-tropomyosin complex | |||||||||
Map data | Reconstruction of F-actin tropomyosin complex | |||||||||
Sample |
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Keywords | F-actin / tropomyosin / filament / protein polymers / muscle / thin filament / cytoskeleton | |||||||||
Function / homology | Function and homology information positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / Striated Muscle Contraction / Smooth Muscle Contraction / muscle filament sliding / actin filament capping / ruffle organization / ventricular cardiac muscle tissue morphogenesis / cytoskeletal motor activator activity / myofibril ...positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / Striated Muscle Contraction / Smooth Muscle Contraction / muscle filament sliding / actin filament capping / ruffle organization / ventricular cardiac muscle tissue morphogenesis / cytoskeletal motor activator activity / myofibril / 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 / positive regulation of cell adhesion / actin monomer binding / skeletal muscle fiber development / cardiac muscle contraction / stress fiber / titin binding / positive regulation of stress fiber assembly / actin filament polymerization / negative regulation of cell migration / filopodium / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / wound healing / structural constituent of cytoskeleton / actin filament binding / calcium-dependent protein binding / disordered domain specific binding / actin cytoskeleton / lamellipodium / actin binding / cell body / in utero embryonic development / hydrolase activity / protein domain specific binding / protein heterodimerization activity / calcium ion binding / positive regulation of gene expression / magnesium ion binding / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Mus musculus (house mouse) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | von der Ecken J / Mueller M / Lehman W / Manstein DJ / Penczek PA / Raunser S | |||||||||
Citation | Journal: Nature / Year: 2015 Title: Structure of the F-actin-tropomyosin complex. Authors: Julian von der Ecken / Mirco Müller / William Lehman / Dietmar J Manstein / Pawel A Penczek / Stefan Raunser / Abstract: Filamentous actin (F-actin) is the major protein of muscle thin filaments, and actin microfilaments are the main component of the eukaryotic cytoskeleton. Mutations in different actin isoforms lead ...Filamentous actin (F-actin) is the major protein of muscle thin filaments, and actin microfilaments are the main component of the eukaryotic cytoskeleton. Mutations in different actin isoforms lead to early-onset autosomal dominant non-syndromic hearing loss, familial thoracic aortic aneurysms and dissections, and multiple variations of myopathies. In striated muscle fibres, the binding of myosin motors to actin filaments is mainly regulated by tropomyosin and troponin. Tropomyosin also binds to F-actin in smooth muscle and in non-muscle cells and stabilizes and regulates the filaments there in the absence of troponin. Although crystal structures for monomeric actin (G-actin) are available, a high-resolution structure of F-actin is still missing, hampering our understanding of how disease-causing mutations affect the function of thin muscle filaments and microfilaments. Here we report the three-dimensional structure of F-actin at a resolution of 3.7 Å in complex with tropomyosin at a resolution of 6.5 Å, determined by electron cryomicroscopy. The structure reveals that the D-loop is ordered and acts as a central region for hydrophobic and electrostatic interactions that stabilize the F-actin filament. We clearly identify map density corresponding to ADP and Mg(2+) and explain the possible effect of prominent disease-causing mutants. A comparison of F-actin with G-actin reveals the conformational changes during filament formation and identifies the D-loop as their key mediator. We also confirm that negatively charged tropomyosin interacts with a positively charged groove on F-actin. Comparison of the position of tropomyosin in F-actin-tropomyosin with its position in our previously determined F-actin-tropomyosin-myosin structure reveals a myosin-induced transition of tropomyosin. Our results allow us to understand the role of individual mutations in the genesis of actin- and tropomyosin-related diseases and will serve as a strong foundation for the targeted development of drugs. | |||||||||
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_6124.map.gz | 5.5 MB | EMDB map data format | |
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Header (meta data) | emd-6124-v30.xml emd-6124.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_6124.jpg | 210.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6124 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6124 | HTTPS FTP |
-Validation report
Summary document | emd_6124_validation.pdf.gz | 316.8 KB | Display | EMDB validaton report |
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Full document | emd_6124_full_validation.pdf.gz | 316.3 KB | Display | |
Data in XML | emd_6124_validation.xml.gz | 4.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6124 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6124 | HTTPS FTP |
-Related structure data
Related structure data | 3j8aMC M: atomic model generated by this map 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_6124.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of F-actin tropomyosin complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.12 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 : F-actin-tropomyosin complex
Entire | Name: F-actin-tropomyosin complex |
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Components |
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-Supramolecule #1000: F-actin-tropomyosin complex
Supramolecule | Name: F-actin-tropomyosin complex / type: sample / ID: 1000 / Oligomeric state: filament / Number unique components: 2 |
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-Macromolecule #1: F-actin (alpha)
Macromolecule | Name: F-actin (alpha) / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Oligomeric state: filament / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / synonym: rabbit / Tissue: muscle |
Sequence | UniProtKB: Actin, alpha skeletal muscle |
-Macromolecule #2: tropomyosin (alpha)
Macromolecule | Name: tropomyosin (alpha) / type: protein_or_peptide / ID: 2 / Oligomeric state: filament (dimer) / Recombinant expression: Yes |
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Source (natural) | Organism: Mus musculus (house mouse) / synonym: mouse / Tissue: muscle |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | UniProtKB: Tropomyosin alpha-1 chain |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 / Details: 5 mM Tris, 1 mM DTT, 100 mM KCL, 2 mM MgCl2 |
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Grid | Details: C-flats 2/1 copper 300 mesh, Protochips, glow-discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 106 K / Instrument: GATAN CRYOPLUNGE 3 Method: Sample was applied to grid, incubated for 10 seconds, and manually blotted for 3 seconds from the backside with filter paper. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Cs | 0 |
Details | Cs-corrected microscope |
Date | Oct 17, 2013 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 1311 / Average electron dose: 14.6 e/Å2 Details: Every image is the average of seven frames recorded by the direct electron detector after beam-induced motion correction. Only 689 images were used for the refinement. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000 / Cs: mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 27.5 Å Applied symmetry - Helical parameters - Δ&Phi: 166.4 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: OTHER / Software - Name: SPARX Details: The tropomyosin map filtered to 6.5 Angstrom was merged with the final F-actin map (3.7 Angstrom) to obtain a map of the entire F-actin tropomyosin complex. |
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CTF correction | Details: each micrograph |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E |
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Software | Name: SPARX, PHENIX, COOT |
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT / Overall B value: 55.4 / Target criteria: R-factor |
Output model | PDB-3j8a: |