+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5752 | |||||||||
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Title | Cryogenic electron microscopy of cardiac actin:tropomyosin | |||||||||
Map data | Reconstruction of rabbit skeletal F-actin and bovine cardiac (striated) tropomyosin. The map is filtered at 15 Angstrom resolution. | |||||||||
Sample |
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Keywords | coiled-coil / actin-binding protein / cytoskeleton | |||||||||
Function / homology | Function and homology information cardiac myofibril / 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 ...cardiac myofibril / 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 / actin monomer binding / skeletal muscle fiber development / muscle contraction / cardiac muscle contraction / stress fiber / titin binding / actin filament polymerization / sarcomere / filopodium / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / calcium-dependent protein binding / disordered domain specific binding / actin cytoskeleton / lamellipodium / actin binding / cell body / hydrolase activity / protein domain specific binding / protein heterodimerization activity / calcium ion binding / positive regulation of gene expression / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 15.0 Å | |||||||||
Authors | Sousa DR / Stagg SM / Stroupe ME | |||||||||
Citation | Journal: J Mol Biol / Year: 2013 Title: Cryo-EM structures of the actin:tropomyosin filament reveal the mechanism for the transition from C- to M-state. Authors: Duncan R Sousa / Scott M Stagg / M Elizabeth Stroupe / Abstract: Tropomyosin (Tm) is a key factor in the molecular mechanisms that regulate the binding of myosin motors to actin filaments (F-Actins) in most eukaryotic cells. This regulation is achieved by the ...Tropomyosin (Tm) is a key factor in the molecular mechanisms that regulate the binding of myosin motors to actin filaments (F-Actins) in most eukaryotic cells. This regulation is achieved by the azimuthal repositioning of Tm along the actin (Ac):Tm:troponin (Tn) thin filament to block or expose myosin binding sites on Ac. In striated muscle, including involuntary cardiac muscle, Tm regulates muscle contraction by coupling Ca(2+) binding to Tn with myosin binding to the thin filament. In smooth muscle, the switch is the posttranslational modification of the myosin. Depending on the activation state of Tn and the binding state of myosin, Tm can occupy the blocked, closed, or open position on Ac. Using native cryogenic 3DEM (three-dimensional electron microscopy), we have directly resolved and visualized cardiac and gizzard muscle Tm on filamentous Ac in the position that corresponds to the closed state. From the 8-Å-resolution structure of the reconstituted Ac:Tm filament formed with gizzard-derived Tm, we discuss two possible mechanisms for the transition from closed to open state and describe the role Tm plays in blocking myosin tight binding in the closed-state position. | |||||||||
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_5752.map.gz | 211.3 KB | EMDB map data format | |
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Header (meta data) | emd-5752-v30.xml emd-5752.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_5752_1.jpg | 53.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5752 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5752 | HTTPS FTP |
-Validation report
Summary document | emd_5752_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_5752_full_validation.pdf.gz | 77.7 KB | Display | |
Data in XML | emd_5752_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5752 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5752 | HTTPS FTP |
-Related 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_5752.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of rabbit skeletal F-actin and bovine cardiac (striated) tropomyosin. The map is filtered at 15 Angstrom resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.477 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 : rabbit skeletal F-actin bound to bovine cardiac tropomyosin
Entire | Name: rabbit skeletal F-actin bound to bovine cardiac tropomyosin |
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Components |
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-Supramolecule #1000: rabbit skeletal F-actin bound to bovine cardiac tropomyosin
Supramolecule | Name: rabbit skeletal F-actin bound to bovine cardiac tropomyosin type: sample / ID: 1000 Oligomeric state: fourteen actin monomers bind to two tropomyosin coiled-coils Number unique components: 2 |
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-Macromolecule #1: Actin, alpha skeletal muscle
Macromolecule | Name: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Name.synonym: Alpha-actin-1 Details: F-actin filaments were formed and tropomyosin was bound to the filaments. Oligomeric state: filament / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: skeletal muscle |
Molecular weight | Experimental: 728 KDa |
Sequence | UniProtKB: Actin, alpha skeletal muscle / GO: skeletal muscle thin filament assembly / InterPro: Actin family |
-Macromolecule #2: Tropomyosin alpha-1
Macromolecule | Name: Tropomyosin alpha-1 / type: protein_or_peptide / ID: 2 / Name.synonym: Alpha-tropomyosin, Tropomyosin-1 Details: F-actin filaments were formed and tropomyosin was bound to the filaments. Oligomeric state: filament / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Bos taurus (cattle) / synonym: Bovine / Tissue: cardiac |
Molecular weight | Experimental: 728 KDa |
Sequence | UniProtKB: Tropomyosin alpha-1 chain / GO: actin binding / InterPro: Tropomyosin |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.1 Details: 70 mM NaCl, 3 mM MgCl2, 0.2 mM EGTA, 5 mM NaH2PO4, 5 mM PIPES buffer |
Grid | Details: Quantifoil 1.2/1.3 sized holes |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV Method: Blot with calcium-free filter paper for 2.5 seconds before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Mar 25, 2010 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 500 / Average electron dose: 30 e/Å2 Details: Images are recorded on a Gatan Ultrascan 4000 CCD and are available upon request to MES (mestroupe@bio.fsu.edu) |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 101555 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Filaments were selected by hand via points along each filament and then boxed at even intervals. |
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CTF correction | Details: Micrograph |
Final reconstruction | Applied symmetry - Helical parameters - Δz: 27.5 Å Applied symmetry - Helical parameters - Δ&Phi: 166.6 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Matlab, SPIDER, EMAN / Number images used: 49318 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: B / Chain - #1 - Chain ID: H |
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Software | Name: Chimera Fit-in-Map |
Details | The F-actin and tropomyosin were fitted separately. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross correlation |