<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-16811" version="3.0.3.0">
    <admin>
        <current_status>
            <date>2023-04-19</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2023-03-09</deposition>
            <header_release>2023-04-19</header_release>
            <map_release>2023-04-19</map_release>
            <update>2023-04-19</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Medical Research Council (MRC, United Kingdom)</funding_body>
                <code>MC_UP_A025_1011</code>
                <country>United Kingdom</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Wellcome Trust</funding_body>
                <code>210711/Z/18/Z</code>
                <country>United Kingdom</country>
            </grant_reference>
        </grant_support>
        <title>Tomogram of an induced protrusion of a cofilin knock-down Drosophila S2 cell with a filament inside the microtubule lumen.</title>
        <authors_list>
            <author ORCID="0000-0002-4406-5151">Ventura Santos C</author>
            <author ORCID="0000-0002-4406-5151">Carter AP</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0002-4406-5151" order="1">Santos CV</author>
                    <author order="2">Rogers SL</author>
                    <author ORCID="0000-0001-7292-5430" order="3">Carter AP</author>
                    <title>CryoET shows cofilactin filaments inside the microtubule lumen.</title>
                    <journal_abbreviation>Biorxiv</journal_abbreviation>
                    <country>US</country>
                    <year>2023</year>
                    <external_references type="PUBMED">37034688</external_references>
                    <external_references type="DOI">doi:10.1101/2023.03.31.535077</external_references>
                    <external_references type="ISSN">2692-8205</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-16800</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>Tomogram of an induced protrusion of a cofilin knock-down Drosophila S2 cell</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-16811</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Tomogram of an induced protrusion of a cofilin knock-down Drosophila S2 cell.</name>
        <supramolecule_list>
            <cell_supramolecule supramolecule_id="1">
                <name>Tomogram of an induced protrusion of a cofilin knock-down Drosophila S2 cell.</name>
                <parent>0</parent>
                <details>Cofilin levels were reduced by siRNA depletion for 7 - 8 days. Cells were then treated with 2 uM thapsigargin for 5 hours and with 2.5 uM Cytochalasin D for 2 hours before vitrification.</details>
                <natural_source database="NCBI">
                    <organism ncbi="7227">Drosophila melanogaster</organism>
                    <strain>S2 cells</strain>
                </natural_source>
            </cell_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>tomography</method>
            <aggregation_state>cell</aggregation_state>
            <specimen_preparation_list>
                <tomography_preparation preparation_id="1">
                    <buffer>
                        <ph>7.0</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">95</chamber_humidity>
                        <chamber_temperature units="K">298.15</chamber_temperature>
                        <instrument>FEI VITROBOT MARK III</instrument>
                    </vitrification>
                    <details>Cofilin levels were reduced by siRNA depletion for 7 - 8 days. Cells were then treated with 2 uM thapsigargin for 5 hours and with 2.5 uM Cytochalasin D for 2 hours before vitrification.</details>
                    <fiducial_markers_list>
                        <fiducial_marker>
                            <manufacturer>BBI Solutions</manufacturer>
                            <diameter units="nanometer">10</diameter>
                        </fiducial_marker>
                    </fiducial_markers_list>
                    <sectioning>
                        <other_sectioning>NO SECTIONING</other_sectioning>
                    </sectioning>
                </tomography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <tomography_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">300</acceleration_voltage>
                    <nominal_defocus_min units="µm">2.5</nominal_defocus_min>
                    <nominal_defocus_max units="µm">6.0</nominal_defocus_max>
                    <specialist_optics>
                        <energy_filter>
                            <name>GIF Bioquantum</name>
                            <slit_width units="eV">20</slit_width>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K3 (6k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <average_electron_dose_per_image units="e/Å^2">3.0</average_electron_dose_per_image>
                            <details>Data was collected on Gatan K3 (2.659 A/pixel) with a total dose of 111.61 e/A2.</details>
                        </image_recording>
                    </image_recording_list>
                </tomography_microscopy>
            </microscopy_list>
            <tomography_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <number_images_used>41</number_images_used>
                </final_reconstruction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="2201634">
        <file>emd_16811.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>1022</col>
            <row>1440</row>
            <sec>374</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>1022</x>
            <y>1440</y>
            <z>374</z>
        </spacing>
        <cell>
            <a units="Å">10874.08</a>
            <b units="Å">15321.601</b>
            <c units="Å">3979.36</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>-0.4719461</minimum>
            <maximum>0.43866646</maximum>
            <average>-1.7506196e-13</average>
            <std>0.037161116</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">10.64</x>
            <y units="Å">10.64</y>
            <z units="Å">10.64</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-16811::::</label>
        <annotation_details>Deconvolved tomogram (binned by four) of an induced protrusion from a cofilin knock-down Drosophila S2 cell. From Dataset 11 part 2.</annotation_details>
    </map>
</emd>
