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Structure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 3)
by helical reconstruction, at 7.7 A resolution
#1: Surface view with section colored by density value, Surface level: 0.0125, Made by UCSF CHIMERA
#2: Surface view colored by cylindrical radius, Surface level: 0.0125, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-4a7f, Surface level: 0.0125, Made by UCSF CHIMERA
#4: Simplified surface model with fitted atomic model: PDB-4a7f, Made by Jmol
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1987 |
|---|---|
| Authors | Behrmann E, Mueller M, Penczek PA, Mannherz HG, Manstein DJ, Raunser S |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 0.0125, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 0.0125, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-4a7f, Surface level: 0.0125, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-4a7f, Made by Jmol |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: output model of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | Cell, Vol. 150, Issue 2, Page 327-38, Year 2012 |
|---|---|
| Title | Structure of the rigor actin-tropomyosin-myosin complex. |
| Authors | Elmar Behrmann, Mirco Müller, Pawel A Penczek, Hans Georg Mannherz, Dietmar J Manstein, Stefan Raunser Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany. |
| Keywords |  Actins (chemistry), Animals, Cryoelectron Microscopy, Humans, Models, Molecular, Multiprotein Complexes (chemistry), Muscle, Skeletal (metabolism), Muscular Diseases (genetics), Myosins (chemistry, 3.6.4.1), Rabbits, Tropomyosin (chemistry) |
| Links | PII: S0092-8674(12)00707-6, DOI: 10.1016/j.cell.2012.05.037, PubMed: 22817895 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1987.map ( map file in CCP4 format, 22530 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A = 294.4 A , B = 294.4 A , C = 404.80002 A , alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 1.84 A , Y = 1.84 A , Z = 1.84 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Conformation 3 of the F-actin-myo1E-tropomyosin complex | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | F-actin-myo1E-tropomyosin complex (conformation 3) |
|---|---|
| Number of Components | 3 |
| Oligomeric State | Pentameric |
| Details | 7 to 7 to 1 (actin to myosin to tropomyosin) |
| Component #1: protein - actin filament | |
| Scientific name | F-actin |
| Common Name | actin filament |
| Oligomeric Details | Filament |
| Number of Copies | 14 |
| Scientific Name of Species | Oryctolagus cuniculus (NCBI Taxonomy: 9986)
|
| Common Name of Species | Rabbit |
| Recombinant expression | No |
| Natural Source | Cell Location: Sarcoplasm Organ Or Tissue: Skeletal muscle |
| Links | Gene Ontology: GO:0042643, InterPro: IPR:004000 |
| Component #2: protein - tropomyosin 1 (alpha) | |
| Scientific name | tropomyosin 1 (alpha) |
| Oligomeric Details | Filament of dimers |
| Number of Copies | 2 |
| Scientific Name of Species | Gallus gallus (NCBI Taxonomy: 9031)
|
| Common Name of Species | Chicken |
| Recombinant expression | Yes |
| Natural Source | Organ Or Tissue: Gizzard |
| Engineered Source | Vector: pJC20 Exp System: Escherichia coli (strain BL21 DE3) |
| Links | InterPro: IPR:000533, Gene Ontology: GO:0005862 |
| Component #3: protein - myosin 1E | |
| Scientific name | myoE |
| Common Name | myosin 1E |
| Oligomeric Details | filament |
| Number of Copies | 14 |
| Scientific Name of Species | Dictyostelium discoideum (NCBI Taxonomy: 44689)
|
| Common Name of Species | Slime mold |
| Strain | AX2 |
| Recombinant expression | Yes |
| Engineered Source | Vector: pDXA-3H Exp System: Dictyostelium discoideum (NCBI Taxonomy: 44689) |
| Links | Gene Ontology: GO:0045160, InterPro: IPR:001609 |
 Experiment | |
| Sample Preparation | |
| Helical Parameters | Delta Z: 27.6 A Delta Phi: 166.5 degrees Hand: LEFT HANDED |
|---|---|
| Specimen Conc | 0.01 mg/ml |
| Specimen Support Details | C-Flat CF-2/1-4C copper 400 mesh |
| Specimen State | filament |
| Buffer | pH: 7.2 Details: 5mM Tris, 100mM KCl, 2mM MgCl2, 50mM glutamine, 50mM arginine |
| Vitrification | |
| Method | Manual blotting for approximately 15 seconds |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Gatan Cryoplunge 3 |
| Humidity | 90 |
| Instrument | GATAN CRYOPLUNGE 3 |
| Temperature | 101 Kelvin |
| Imaging | |
| Microscope | JEOL 3200FSC |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 17 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 80000 X, Calibrated: 169644 X |
| Astigmatism | objective lens astigmatism was corrected at 150,000 times magnification |
| Nominal Cs | 4.1 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 750 nm - 1500 nm |
| Energy Filter | Type: in-column Omega filter , Window: 0-12 eV |
| Specimen Holder | |
| Holder | cryogenic stage with side entry access ( JEOL 3200FSC CRYOHOLDER ) |
| Temperature | 77 Kelvin |
| Camera | |
| Detector | TemCam-F816 |
| Image Acquisition | |
| Number of Digital Images | 836 |
| Sampling Size | 15.6 microns |
| Quant Bit Number | 14 |
| Details | Over 3000 images were taken of which only the best 836 were used for processing |
 Processing | |
| Method | helical reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | IHRSR |
| Software | SPARX |
| CTF Correction | each particle |
| Details | Particles were classified using CODIM |
| Resolution By Author | 7.7 |
| Resolution Method | FSC at 0.5 cut-off |
| Helical | |
| Details | Particles were selected by hand using e2helixboxer |
| Atomic Model Fitting | |
| Model #0 | |
| Details | Protocol: geometry-based conformational sampling using Deformable Elastic Network (DEN) approach. Initial placement was performed using rigid-body fitting in Chimera |
| Software | DireX |
| Refinement Protocol | flexible |
| Refinement Space | REAL |
| Fitted Coordinate | |
| PDB entry ID | |
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Detail page - EMDB-1987
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