|Entry||Database: EMDB / ID: 1987|
|Title||Structure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 3)|
|Keywords||Structural protein / cytoskeleton / contractile filament / motor activity / myosin binding / actin binding / ATP catabolic process / rigor state|
|Sample||F-actin-myo1E-tropomyosin complex (conformation 3)|
|Source||Oryctolagus cuniculus / mammal / Rabbit / アナウサギ / |
Gallus gallus / bird / Chicken / ウズラチャボ, オナガドリ, セキショクヤケイ, トウマル /
Dictyostelium discoideum / fungus / Slime mold /
|Map data||Conformation 3 of the F-actin-myo1E-tropomyosin complex|
|Method||helical reconstruction, at 7.7 Å resolution|
|Authors||Behrmann E / Mueller M / Penczek PA / Mannherz HG / Manstein DJ / Raunser S|
|Citation||Cell, 2012, 150, 327-338|
|Validation Report||PDB-ID: 4a7f|
About validation report
|Date||Deposition: Nov 14, 2011 / Header (metadata) release: Aug 1, 2012 / Map release: Aug 1, 2012 / Last update: Aug 1, 2012|
Downloads & links
|File||emd_1987.map.gz (map file in CCP4 format, 22001 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.84 Å|
CCP4 map header:
-Entire F-actin-myo1E-tropomyosin complex (conformation 3)
|Entire||Name: F-actin-myo1E-tropomyosin complex (conformation 3) / Details: 7 to 7 to 1 (actin to myosin to tropomyosin) / Number of components: 3 / Oligomeric State: Pentameric|
-Component #1: protein, F-actin
|Protein||Name: F-actin / a.k.a: actin filament / Oligomeric Details: Filament / Number of Copies: 14 / Recombinant expression: No|
|Source||Species: Oryctolagus cuniculus / mammal / Rabbit / アナウサギ /|
|Source (natural)||Location in cell: Sarcoplasm / Organ or tissue: Skeletal muscle|
|External references||Gene Ontology: GO: 0042643 / InterPro: InterPro: 004000|
-Component #2: protein, tropomyosin 1 (alpha)
|Protein||Name: tropomyosin 1 (alpha) / a.k.a: tropomyosin 1 (alpha) / Oligomeric Details: Filament of dimers / Recombinant expression: Yes / Number of Copies: 2|
|Source||Species: Gallus gallus / bird / Chicken / ウズラチャボ, オナガドリ, セキショクヤケイ, トウマル /|
|Source (engineered)||Expression System: Escherichia coli (strain bl21 de3) / bacteria / |
|Source (natural)||Organ or tissue: Gizzard|
|External references||InterPro: InterPro: 000533 / Gene Ontology: GO: 0005862|
-Component #3: protein, myoE
|Protein||Name: myoE / a.k.a: myosin 1E / Oligomeric Details: filament / Recombinant expression: Yes / Number of Copies: 14|
|Source||Species: Dictyostelium discoideum / fungus / Slime mold / / Strain: AX2|
|Source (engineered)||Expression System: Dictyostelium discoideum / fungus / / Vector: pDXA-3H|
|External references||Gene Ontology: GO: 0045160 / InterPro: InterPro: 001609|
|Helical parameters||Hand: LEFT HANDED / Delta z: 27.6 Å / Delta phi: 166.5 deg.|
|Sample solution||Specimen conc.: 0.01 mg/ml|
Buffer solution: 5mM Tris, 100mM KCl, 2mM MgCl2, 50mM glutamine, 50mM arginine
|Support film||C-Flat CF-2/1-4C copper 400 mesh|
|Vitrification||Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 101 K / Humidity: 90 % / Method: Manual blotting for approximately 15 seconds / Details: Vitrification instrument: Gatan Cryoplunge 3|
-Electron microscopy imaging
|Imaging||Microscope: JEOL 3200FSC|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 17 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 80000 X (nominal), 169644 X (calibrated)|
Astigmatism: objective lens astigmatism was corrected at 150,000 times magnification
Cs: 4.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 750 - 1500 nm / Energy filter: in-column Omega filter / Energy window: 0-12 eV
|Specimen Holder||Holder: cryogenic stage with side entry access / Model: JEOL 3200FSC CRYOHOLDER / Temperature: 77 K|
|Camera||Detector: TVIPS TEMCAM-F816 (8k x 8k)|
|Image acquisition||Number of digital images: 836 / Sampling size: 15.6 microns / Bit depth: 14|
Details: Over 3000 images were taken of which only the best 836 were used for processing
|Processing||Method: helical reconstruction / Details: Particles were selected by hand using e2helixboxer|
|3D reconstruction||Algorithm: IHRSR / Software: SPARX / CTF correction: each particle / Details: Particles were classified using CODIM / Resolution: 7.7 Å / Resolution method: FSC 0.5|
-Atomic model buiding
|Modeling #1||Software: DireX / Refinement protocol: flexible / Refinement space: REAL|
Details: Protocol: geometry-based conformational sampling using Deformable Elastic Network (DEN) approach. Initial placement was performed using rigid-body fitting in Chimera
Input PDB model: 1LKX
Chain ID: 1LKX_C
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