<emd emdb_id="EMD-2610" 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>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2014-03-21</deposition>
            <header_release>2014-04-30</header_release>
            <map_release>2015-04-15</map_release>
            <update>2015-05-13</update>
        </key_dates>
        <title>Electron tomography of zipping in Drosophyla melanogaster</title>
        <authors_list>
            <author>Eltsov M</author>
            <author>Dube N</author>
            <author>Yu Z</author>
            <author>Haselmann-Weiss U</author>
            <author>Brunner D</author>
            <author>Frangakis A S</author>
        </authors_list>
        <keywords>epithelial tissue sealing, dorsal closure, serial tomography, high pressure freezing, freeze-substitution</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Eltsov M</author>
                    <author order="2">Dube N</author>
                    <author order="3">Yu Z</author>
                    <author order="4">Haselmann-Weiss U</author>
                    <author order="5">Brunner D</author>
                    <author order="6">Frangakis A S</author>
                    <title>Quantitative analysis of cytoskeletal reorganization during epithelial tissue sealing by large-volume electron tomography.</title>
                    <journal>NAT.CELL BIOL.</journal>
                    <volume>17</volume>
                    <first_page>605</first_page>
                    <last_page>614</last_page>
                    <year>2015</year>
                    <external_references type="PUBMED">25893916</external_references>
                    <external_references type="DOI">doi:10.1038/ncb3159</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Tomographic reconstruction of an entire zipping in Drosophila embryo</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Tomographic reconstruction of an entire zipping in Drosophila embryo</name>
                <details>Joined 34 serial tomograms were reconstructed from 2x2 montaged tilt-series. Tilt-series were recorded at x12000 corresponding to 0.9nm/pixel at the specimen level. The map was binned for deposition to reduce the file size.
The z-axis of the map corresponds to the anterior/posterior embryonic axis while the y-axis to the ventral/dorsal axis. The dorsal epidermal cells are located on the top.</details>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name>zipping in Drosphila embryogenesis</name>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <natural_source database="NCBI">
                    <organism ncbi="7227">Drosophila melanogaster</organism>
                    <synonym_organism>fruit fly</synonym_organism>
                </natural_source>
                <recombinant_expression database="NCBI" />
            </organelle_or_cellular_component_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>tomography</method>
            <aggregation_state>tissue</aggregation_state>
            <specimen_preparation_list>
                <tomography_preparation preparation_id="1">
                    <staining>
                        <type>NEGATIVE</type>
                        <details>Sections were stained with 2% UA in 70% methanol and Reynolds lead citrate.</details>
                    </staining>
                    <grid>
                        <details>slot grids with Formvar support</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>NITROGEN</cryogen_name>
                        <instrument>OTHER</instrument>
                    </vitrification>
                </tomography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <tomography_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F30</microscope>
                    <illumination_mode>OTHER</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <nominal_magnification>12000.0</nominal_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <date>2010-05-10</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">FEI EAGLE (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <scanner>OTHER</scanner>
                            </digitization_details>
                        </image_recording>
                    </image_recording_list>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">-60</min_angle>
                            <max_angle units="deg">60</max_angle>
                            <angle_increment units="deg">1.5</angle_increment>
                        </axis1>
                    </tilt_series>
                </tomography_microscopy>
            </microscopy_list>
            <tomography_processing image_processing_id="1">
                <final_reconstruction>
                    <software_list>
                        <software>
                            <name>ETOMO</name>
                        </software>
                    </software_list>
                    <number_images_used>120</number_images_used>
                </final_reconstruction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="1091261">
        <file>emd_2610.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS SIGNED BYTE</data_type>
        <dimensions>
            <col>892</col>
            <row>999</row>
            <sec>1254</sec>
        </dimensions>
        <origin>
            <col>-52</col>
            <row>957</row>
            <sec>14</sec>
        </origin>
        <spacing>
            <x>999</x>
            <y>892</y>
            <z>1254</z>
        </spacing>
        <cell>
            <a units="&#8491;">52628.0</a>
            <b units="&#8491;">58941.0</b>
            <c units="&#8491;">101574.0</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>-128.0</minimum>
            <maximum>127.0</maximum>
            <average>1.30015326</average>
            <std>30.184339520000002</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">59.0</x>
            <y units="&#8491;">59.0</y>
            <z units="&#8491;">81.0</z>
        </pixel_spacing>
        <annotation_details>Tomographic reconstruction of Drosophila zipping</annotation_details>
        <details>::::EMDATABANK.org::::EMD-2610::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_2610.tif</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>