<?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_10_1/emdb.xsd" version="3.0.10.1" emdb_id="EMD-19645">
    <admin>
        <current_status>
            <date>2025-04-30</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <revision_history>
            <revision version="1.0" date="2025-03-05">
                <change_list>
                    <metadata>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </metadata>
                    <image>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </image>
                    <primary_map>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </primary_map>
                </change_list>
            </revision>
        </revision_history>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2024-02-16</deposition>
            <header_release>2025-03-05</header_release>
            <map_release>2025-03-05</map_release>
            <update>2025-04-30</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Max Planck Society</funding_body>
                <country>Germany</country>
            </grant_reference>
        </grant_support>
        <title>Tomographic reconstruction of the follicle cell nuclear periphery from high pressure frozen, freeze substituted and resin embedded D. melanogaster egg chamber</title>
        <authors_list>
            <author>Klumpe S</author>
            <author>Hampoelz B</author>
            <author>Ronchi P</author>
            <author>Beck M</author>
            <author>Plitzko J</author>
        </authors_list>
        <keywords>Tomography, Drosophila, melanogaster, follicle cell, nuclear periphery, nucleus, freeze-substitution, VIRUS LIKE PARTICLE</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Klumpe S</author>
                    <author order="2">Senti KA</author>
                    <author order="3">Beck F</author>
                    <author order="4">Sachweh J</author>
                    <author order="5">Hampoelz B</author>
                    <author order="6">Ronchi P</author>
                    <author order="7">Oorschot V</author>
                    <author order="8">Brandstetter M</author>
                    <author order="9">Yeroslaviz A</author>
                    <author order="10">Briggs JAG</author>
                    <author order="11">Brennecke J</author>
                    <author order="12">Beck M</author>
                    <author order="13">Plitzko JM</author>
                    <title>In-cell structure and snapshots of copia retrotransposons in intact tissue by cryo-ET.</title>
                    <journal_abbreviation>Cell</journal_abbreviation>
                    <volume>188</volume>
                    <first_page>2094</first_page>
                    <last_page>2110.e18</last_page>
                    <year>2025</year>
                    <external_references type="PUBMED">40049165</external_references>
                    <external_references type="DOI">doi:10.1016/j.cell.2025.02.003</external_references>
                    <external_references type="ISSN">1097-4172</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>D. melanogaster egg chamber 
from tj&gt;Sec31::RFP flies</name>
        <supramolecule_list>
            <tissue_supramolecule supramolecule_id="1">
                <name>D. melanogaster egg chamber 
from tj&gt;Sec31::RFP flies</name>
                <parent>0</parent>
                <details>Females from F1 scored against CyO from following genotypes:
traffic jam-GAL4/CyO;; and
 w* P{UAS-Sec31.RFP}13.5; snaSco/CyO, P{ftz-lacB}E3  (Bloomington #86533);</details>
                <natural_source database="NCBI">
                    <organism ncbi="7227">Drosophila melanogaster</organism>
                    <organ>Egg chamber</organ>
                    <tissue>Follicle cell epithelium</tissue>
                </natural_source>
            </tissue_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">
                    <buffer>
                        <ph>7.4</ph>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <material>Uranyl Acetate</material>
                    </staining>
                    <sugar_embedding>
                        <material>Lowicryl HM20</material>
                    </sugar_embedding>
                    <vitrification>
                        <cryogen_name>NITROGEN</cryogen_name>
                    </vitrification>
                    <details>Dissected egg chambers</details>
                    <high_pressure_freezing>
                        <instrument>OTHER</instrument>
                        <details>The value given for _em_high_pressure_freezing.instrument is HPM 010. This is not in a list of allowed values {'EMS-002 RAPID IMMERSION FREEZER', 'BAL-TEC HPM 010', 'OTHER', 'LEICA EM HPM100', 'LEICA EM PACT2', 'LEICA EM PACT'} so OTHER is written into the XML file.</details>
                    </high_pressure_freezing>
                    <cryo_protectant>20% Ficoll 70 kDa</cryo_protectant>
                    <sectioning>
                        <ultramicrotomy>
                            <instrument>Leica EM UC7</instrument>
                            <temperature units="K">293</temperature>
                            <final_thickness>300</final_thickness>
                        </ultramicrotomy>
                    </sectioning>
                </tomography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <tomography_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F30</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">0.5</nominal_defocus_min>
                    <nominal_defocus_max units="µm">0.5</nominal_defocus_max>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>OTHER</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">10.0</average_electron_dose_per_image>
                            <details>Gatan OneView</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>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                        </software>
                    </software_list>
                    <number_images_used>121</number_images_used>
                </final_reconstruction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="696255">
        <file>emd_19645.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS SIGNED BYTE</data_type>
        <dimensions>
            <col>2048</col>
            <row>2048</row>
            <sec>166</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>-80</sec>
        </origin>
        <spacing>
            <x>2048</x>
            <y>2048</y>
            <z>166</z>
        </spacing>
        <cell>
            <a units="Å">24985.6</a>
            <b units="Å">24985.6</b>
            <c units="Å">2025.2</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>10.200196999999999</average>
            <std>28.728092</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">12.2</x>
            <y units="Å">12.2</y>
            <z units="Å">12.2</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-19645::::</label>
        <annotation_details>Tomographic reconstruction</annotation_details>
    </map>
</emd>
