<emd emdb_id="EMD-5751" version="3.0.1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_1/emdb_relaxed.xsd">
    <admin>
        <current_status>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2013-08-26</deposition>
            <header_release>2013-09-18</header_release>
            <map_release>2013-09-18</map_release>
            <update>2016-03-02</update>
        </key_dates>
        <title>Cryogenic electron microscopy of cardiac actin:tropomyosin</title>
        <authors_list>
            <author>Sousa DR</author>
            <author>Stagg SM</author>
            <author>Stroupe ME</author>
        </authors_list>
        <keywords>coiled-coil, actin-binding protein, cytoskeleton</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Sousa DR</author>
                    <author order="2">Stagg SM</author>
                    <author order="3">Stroupe ME</author>
                    <title>Cryo-EM Structures of the Actin:Tropomyosin Filament Reveal the Mechanism for the Transition from C- to M-State.</title>
                    <journal>J.MOL.BIOL.</journal>
                    <volume>425</volume>
                    <first_page>4544</first_page>
                    <last_page>4555</last_page>
                    <year>2013</year>
                    <external_references type="PUBMED">24021812</external_references>
                    <external_references type="DOI">doi:10.1016/j.jmb.2013.08.020</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3j4k</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>rabbit skeletal F-actin bound to chicken gizzard tropomyosin</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>rabbit skeletal F-actin bound to chicken gizzard tropomyosin</name>
                <oligomeric_state>fourteen actin monomers bind to two tropomyosin coiled-coils</oligomeric_state>
                <number_unique_components>2</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="Alpha-actin-1">Actin, alpha skeletal muscle</name>
                <natural_source database="NCBI">
                    <organism ncbi="9986">Oryctolagus cuniculus</organism>
                    <synonym_organism>rabbit</synonym_organism>
                    <tissue>skeletal muscle</tissue>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.728</experimental>
                </molecular_weight>
                <details>F-actin filaments were formed and tropomyosin was bound to the filaments.</details>
                <oligomeric_state>filament</oligomeric_state>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence>
                    <external_references type="UNIPROTKB">P68135</external_references>
                    <external_references type="GO">GO:0030240</external_references>
                    <external_references type="INTERPRO">IPR004000</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name synonym="Alpha-tropomyosin, Tropomyosin-1">Tropomyosin alpha-1</name>
                <natural_source database="NCBI">
                    <organism ncbi="9031">Gallus gallus</organism>
                    <synonym_organism>Chicken</synonym_organism>
                    <tissue>gizzard</tissue>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.728</experimental>
                </molecular_weight>
                <details>F-actin filaments were formed and tropomyosin was bound to the filaments.</details>
                <oligomeric_state>filament</oligomeric_state>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence>
                    <external_references type="UNIPROTKB">P19352</external_references>
                    <external_references type="GO">GO:0005862</external_references>
                    <external_references type="INTERPRO">IPR000533</external_references>
                </sequence>
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>singleParticle</method>
            <aggregation_state>filament</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <concentration units="mg/mL">0.5</concentration>
                    <buffer>
                        <ph>7.1</ph>
                        <details>70 mM NaCl, 3 mM MgCl2, 0.2 mM EGTA, 5 mM NaH2PO4, 5 mM PIPES buffer</details>
                    </buffer>
                    <grid>
                        <details>Quantifoil 2/2 sized holes</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">120</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>Blot with calcium-free filter paper for 2.5 seconds before plunging.</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <nominal_defocus_min units="&#181;m">1.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">4.0</nominal_defocus_max>
                    <nominal_magnification>59000.0</nominal_magnification>
                    <calibrated_magnification>101555.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <date>2011-03-02</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <number_real_images>700</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">30</average_electron_dose_per_image>
                            <details>Images are recorded on a Gatan Ultrascan 4000 CCD and are available upon request to MES (mestroupe@bio.fsu.edu)</details>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Filaments were selected by hand via points along each filament and then boxed at even intervals.</details>
                <ctf_correction>
                    <details>Micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">27.5</delta_z>
                            <delta_phi units="deg">166.6</delta_phi>
                            <axial_symmetry>C1</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">8.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>Matlab, SPIDER, EMAN</name>
                        </software>
                    </software_list>
                    <number_images_used>224337</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="65537">
        <file>emd_5751.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>256</col>
            <row>256</row>
            <sec>256</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>256</x>
            <y>256</y>
            <z>256</z>
        </spacing>
        <cell>
            <a units="&#8491;">378.112</a>
            <b units="&#8491;">378.112</b>
            <c units="&#8491;">378.112</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
        </cell>
        <axis_order>
            <fast>X</fast>
            <medium>Y</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-0.10712808</minimum>
            <maximum>32.032436369999999</maximum>
            <average>0.0</average>
            <std>0.99999994</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.477</x>
            <y units="&#8491;">1.477</y>
            <z units="&#8491;">1.477</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.1</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of rabbit skeletal muscle F-actin with chicken gizzard (smooth) muscle tropomyosin. A B-factor of -487 Angstrom^2 and an 8-Angstrom low pass filter were applied.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5751::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>4A7F</access_code>
                    <chain>
                        <chain_id>A</chain_id>
                    </chain>
                    <chain>
                        <chain_id>B</chain_id>
                    </chain>
                    <chain>
                        <chain_id>D</chain_id>
                    </chain>
                    <chain>
                        <chain_id>E</chain_id>
                    </chain>
                    <chain>
                        <chain_id>F</chain_id>
                    </chain>
                    <chain>
                        <chain_id>H</chain_id>
                    </chain>
                    <chain>
                        <chain_id>I</chain_id>
                    </chain>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera Fit-in-Map</name>
                    </software>
                </software_list>
                <details>The F-actin and tropomyosin were fitted separately.</details>
                <target_criteria>Cross correlation</target_criteria>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>