<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-15137" version="3.0.2.8">
    <admin>
        <current_status>
            <date>2023-02-01</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2022-06-10</deposition>
            <header_release>2023-02-01</header_release>
            <map_release>2023-02-01</map_release>
            <update>2023-02-01</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Austrian Science Fund</funding_body>
                <code>P33367</code>
                <country>Austria</country>
            </grant_reference>
        </grant_support>
        <title>Tomogram of a lamellipodium of a WT B16-F1 mouse melanoma cell</title>
        <authors_list>
            <author ORCID="0000-0001-7149-769X">Faessler F</author>
            <author ORCID="0000-0001-7149-769X">Javoor MG</author>
            <author ORCID="0000-0001-7149-769X">Datler J</author>
            <author ORCID="0000-0001-7149-769X">Doering H</author>
            <author ORCID="0000-0001-7149-769X">Hofer FW</author>
            <author ORCID="0000-0001-7149-769X">Dimchev G</author>
            <author ORCID="0000-0001-7149-769X">Hodirnau VV</author>
            <author ORCID="0000-0001-7149-769X">Rottner K</author>
            <author ORCID="0000-0001-7149-769X">Schur FKM</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0001-7149-769X" order="1">Fassler F</author>
                    <author order="2">Javoor MG</author>
                    <author order="3">Datler J</author>
                    <author ORCID="0000-0001-6699-8393" order="4">Doring H</author>
                    <author ORCID="0000-0002-6531-3820" order="5">Hofer FW</author>
                    <author ORCID="0000-0001-8370-6161" order="6">Dimchev G</author>
                    <author ORCID="0000-0003-3904-947X" order="7">Hodirnau VV</author>
                    <author order="8">Faix J</author>
                    <author ORCID="0000-0003-4244-4198" order="9">Rottner K</author>
                    <author ORCID="0000-0003-4790-8078" order="10">Schur FKM</author>
                    <title>ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.</title>
                    <journal_abbreviation>Sci Adv</journal_abbreviation>
                    <country>US</country>
                    <volume>9</volume>
                    <first_page>eadd6495</first_page>
                    <last_page>eadd6495</last_page>
                    <year>2023</year>
                    <external_references type="PUBMED">36662867</external_references>
                    <external_references type="DOI">doi:10.1126/sciadv.add6495</external_references>
                    <external_references type="ISSN">2375-2548</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-15136</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>Corresponding Arp2/3 branch junction structure</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-15137</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Tomogram of a lamellipodium of a WT B16-F1 mouse melanoma cell</name>
        <supramolecule_list>
            <cell_supramolecule supramolecule_id="1">
                <name>Tomogram of a lamellipodium of a WT B16-F1 mouse melanoma cell</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="10090">Mus musculus</organism>
                    <strain>B16-F1</strain>
                    <tissue>Melanoma</tissue>
                </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>6.2</ph>
                        <component>
                            <concentration units="mM">10.0</concentration>
                            <name>MES</name>
                        </component>
                        <component>
                            <concentration units="mM">150.0</concentration>
                            <name>Sodium</name>
                        </component>
                        <component>
                            <concentration units="mM">5.0</concentration>
                            <name>EGTA</name>
                        </component>
                        <component>
                            <concentration units="mM">5.0</concentration>
                            <name>Glucose</name>
                        </component>
                        <component>
                            <concentration units="mM">5.0</concentration>
                            <name>Magnedium chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">200.0</concentration>
                            <name>Glutaraldehyde</name>
                        </component>
                        <details>Adjust to pH 6.2 using NaOH
Immediately prior to use, add Phalloidin to a final concentration of 1ug/ml</details>
                    </buffer>
                    <grid>
                        <model>Quantifoil R2/2</model>
                        <material>GOLD</material>
                        <mesh>200</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <time units="s">120</time>
                            <atmosphere>AIR</atmosphere>
                        </pretreatment>
                        <details>After glow discharging of the grid and prior to the seeding of cells, the grid was coated using 25ug/ml Laminin for 60min</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">80</chamber_humidity>
                        <chamber_temperature units="K">277</chamber_temperature>
                        <instrument>LEICA EM GP</instrument>
                    </vitrification>
                    <fiducial_markers_list>
                        <fiducial_marker>
                            <manufacturer>Aurion</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>
                    <c2_aperture_diameter units="µm">50.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">1.5</nominal_defocus_min>
                    <nominal_defocus_max units="µm">4.5</nominal_defocus_max>
                    <nominal_magnification>53000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <coma_free/>
                    </alignment_procedure>
                    <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>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>67</number_real_images>
                            <average_electron_dose_per_image units="e/Å^2">2.79</average_electron_dose_per_image>
                            <details>Images were collected in movie-mode with 8 frames per tilt</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>
                    <algorithm>BACK PROJECTION</algorithm>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0.8</version>
                        </software>
                    </software_list>
                    <number_images_used>65</number_images_used>
                </final_reconstruction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="294913">
        <file>emd_15137.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>512</col>
            <row>720</row>
            <sec>200</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>512</x>
            <y>720</y>
            <z>200</z>
        </spacing>
        <cell>
            <a units="Å">6934.528</a>
            <b units="Å">9751.68</b>
            <c units="Å">2708.8</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>-0.49811822</minimum>
            <maximum>0.47268265</maximum>
            <average>1.7543996e-05</average>
            <std>0.052847598</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">13.544</x>
            <y units="Å">13.544</y>
            <z units="Å">13.544001</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-15137::::</label>
        <annotation_details>Tomogram of a lamellipodium of a WT B16-F1 mouse melanoma cell</annotation_details>
    </map>
</emd>
