<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://ftp.ebi.ac.uk/pub/databases/em_ebi/emdb_related/emdb-schemas/emdb_schemas/v3/v3_0_11_0/emdb.xsd" version="3.0.11.0" emdb_id="EMD-61088">
    <admin>
        <current_status>
            <date>2025-06-18</date>
            <code>REL</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2024-08-06</deposition>
            <header_release>2024-09-04</header_release>
            <map_release>2024-09-04</map_release>
            <update>2025-06-18</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Japan Society for the Promotion of Science (JSPS)</funding_body>
                <code>21H05254</code>
                <country>Japan</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Japan Society for the Promotion of Science (JSPS)</funding_body>
                <code>18K19328</code>
                <country>Japan</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Japan Society for the Promotion of Science (JSPS)</funding_body>
                <code>18K15002</code>
                <country>Japan</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Japan Society for the Promotion of Science (JSPS)</funding_body>
                <code>20K16105</code>
                <country>Japan</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Japan Society for the Promotion of Science (JSPS)</funding_body>
                <code>22K06219</code>
                <country>Japan</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Japan Society for the Promotion of Science (JSPS)</funding_body>
                <code>22K06809</code>
                <country>Japan</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Japan Society for the Promotion of Science (JSPS)</funding_body>
                <code>22K20680ZA</code>
                <country>Japan</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Japan Society for the Promotion of Science (JSPS)</funding_body>
                <code>23K14178ZA</code>
                <country>Japan</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Japan Society for the Promotion of Science (JSPS)</funding_body>
                <code>23K23823</code>
                <country>Japan</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Japan Society for the Promotion of Science (JSPS)</funding_body>
                <code>23K06674</code>
                <country>Japan</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Japan Agency for Medical Research and Development (AMED)</funding_body>
                <code>JP21gm161003</code>
                <country>Japan</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Japan Science and Technology</funding_body>
                <code>JPMJFR214K</code>
                <country>Japan</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Japan Science and Technology</funding_body>
                <code>JPMJMS2024</code>
                <country>Japan</country>
            </grant_reference>
        </grant_support>
        <title>Cryo-electron tomography of optogenetically-induced lamellipodia</title>
        <authors_list>
            <author ORCID="0000-0002-9622-6017">Inaba H</author>
            <author ORCID="0000-0001-5462-1820">Imasaki T</author>
            <author>Aoyama K</author>
            <author ORCID="0000-0001-8633-7285">Yoshihara S</author>
            <author>Takazaki H</author>
            <author ORCID="0000-0002-8879-6685">Kato T</author>
            <author ORCID="0000-0002-6796-4467">Goto H</author>
            <author ORCID="0000-0003-1782-675X">Mitsuoka K</author>
            <author ORCID="0000-0002-6537-9272">Nitta R</author>
            <author ORCID="0000-0002-0629-0518">Nakata T</author>
        </authors_list>
        <keywords>actin cytoskeleton, plasma membrane, lamellipodia, STRUCTURAL PROTEIN</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Inaba H</author>
                    <author order="2">Imasaki T</author>
                    <author order="3">Aoyama K</author>
                    <author order="4">Yoshihara S</author>
                    <author order="5">Takazaki H</author>
                    <author order="6">Kato T</author>
                    <author order="7">Goto H</author>
                    <author order="8">Mitsuoka K</author>
                    <author order="9">Nitta R</author>
                    <author order="10">Nakata T</author>
                    <title>Cryo-ET of actin cytoskeleton and membrane structure in lamellipodia formation using optogenetics.</title>
                    <journal_abbreviation>Iscience</journal_abbreviation>
                    <country>US</country>
                    <volume>28</volume>
                    <first_page>112529</first_page>
                    <last_page>112529</last_page>
                    <year>2025</year>
                    <external_references type="PUBMED">40475257</external_references>
                    <external_references type="DOI">doi:10.1016/j.isci.2025.112529</external_references>
                    <external_references type="ISSN">2589-0042</external_references>
                </journal_citation>
            </primary_citation>
            <secondary_citation>
                <journal_citation published="true">
                    <author order="11">Inaba H</author>
                    <author order="12">Imasaki T</author>
                    <author order="13">Aoyama K</author>
                    <author order="14">Yoshihara S</author>
                    <author order="15">Takazaki H</author>
                    <author order="16">Kato T</author>
                    <author order="17">Goto H</author>
                    <author order="18">Mitsuoka K</author>
                    <author order="19">Nitta R</author>
                    <author order="20">Nakata T</author>
                    <title>Cryo-electron tomography of the actin cytoskeleton and membrane organization during lamellipodia formation using optogenetics.</title>
                    <journal_abbreviation>Biorxiv</journal_abbreviation>
                    <country>US</country>
                    <year>2024</year>
                    <external_references type="DOI">doi:10.1101/2024.08.13.607852</external_references>
                    <external_references type="ISSN">2692-8205</external_references>
                </journal_citation>
            </secondary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>lamellipodia in COS-7 cells</name>
        <supramolecule_list>
            <cell_supramolecule supramolecule_id="1">
                <name>lamellipodia in COS-7 cells</name>
                <parent>0</parent>
                <details>PA-Rac1 induced lamellipodia</details>
                <natural_source database="NCBI">
                    <organism ncbi="9534">Chlorocebus aethiops</organism>
                    <organ>kidney</organ>
                </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>7.4</ph>
                    </buffer>
                    <grid>
                        <model>Quantifoil R1.2/1.3</model>
                        <material>GOLD</material>
                        <mesh>300</mesh>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                    </vitrification>
                    <fiducial_markers_list>
                        <fiducial_marker>
                            <manufacturer>SIGMA-Aldrich</manufacturer>
                            <diameter units="nanometer">20</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">4.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">4.0</nominal_defocus_max>
                    <specialist_optics>
                        <phase_plate>VOLTA PHASE PLATE</phase_plate>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K3 BIOQUANTUM (6k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">1.44</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </tomography_microscopy>
            </microscopy_list>
            <tomography_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <algorithm>SIMULTANEOUS ITERATIVE (SIRT)</algorithm>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                            <version>4.11.24</version>
                        </software>
                    </software_list>
                    <number_images_used>67</number_images_used>
                </final_reconstruction>
                <ctf_correction>
                    <type>NONE</type>
                </ctf_correction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="746380">
        <file>emd_61088.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>972</col>
            <row>1422</row>
            <sec>135</sec>
        </dimensions>
        <origin>
            <col>51</col>
            <row>8</row>
            <sec>-115</sec>
        </origin>
        <spacing>
            <x>972</x>
            <y>1422</y>
            <z>135</z>
        </spacing>
        <cell>
            <a units="Å">14432.645</a>
            <b units="Å">21114.426</b>
            <c units="Å">2004.534</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>-1408.29099999999994</minimum>
            <maximum>1127.064599999999928</maximum>
            <average>-0.5505246</average>
            <std>57.956142</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">14.8484</x>
            <y units="Å">14.848401</y>
            <z units="Å">14.8484</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-61088::::</label>
    </map>
</emd>
