<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-16085">
    <admin>
        <current_status>
            <date>2023-07-12</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2022-11-02</deposition>
            <header_release>2023-07-12</header_release>
            <map_release>2023-07-12</map_release>
            <update>2023-07-12</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>German Research Foundation (DFG)</funding_body>
                <code>LU 1819/2-1</code>
                <country>Germany</country>
            </grant_reference>
        </grant_support>
        <title>Munc13-SNAP25 cryo-ET dataset, synapse tomo Munc13 DKO 102 (id: m13_dko_102)</title>
        <authors_list>
            <author ORCID="0000-0001-7863-3009">Papantoniou C</author>
            <author ORCID="0000-0003-3698-7436">Lucic V</author>
        </authors_list>
        <keywords>Neuronal synapse, Presynaptic terminal, Tethering, SNARE complex, CELL ADHESION</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0001-7863-3009" order="1">Papantoniou C</author>
                    <author ORCID="0000-0003-4175-4354" order="2">Laugks U</author>
                    <author ORCID="0000-0002-9643-1264" order="3">Betzin J</author>
                    <author ORCID="0000-0002-5297-9156" order="4">Capitanio C</author>
                    <author order="5">Ferrero JJ</author>
                    <author order="6">Sanchez-Prieto J</author>
                    <author ORCID="0000-0002-2046-2670" order="7">Schoch S</author>
                    <author order="8">Brose N</author>
                    <author ORCID="0000-0001-8154-8809" order="9">Baumeister W</author>
                    <author ORCID="0000-0003-2374-9922" order="10">Cooper BH</author>
                    <author ORCID="0000-0001-7351-8706" order="11">Imig C</author>
                    <author ORCID="0000-0003-3698-7436" order="12">Lucic V</author>
                    <title>Munc13- and SNAP25-dependent molecular bridges play a key role in synaptic vesicle priming.</title>
                    <journal_abbreviation>Sci Adv</journal_abbreviation>
                    <country>US</country>
                    <volume>9</volume>
                    <first_page>eadf6222</first_page>
                    <last_page>eadf6222</last_page>
                    <year>2023</year>
                    <external_references type="PUBMED">37343100</external_references>
                    <external_references type="DOI">doi:10.1126/sciadv.adf6222</external_references>
                    <external_references type="ISSN">2375-2548</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-16085</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Synaptosome</name>
        <supramolecule_list>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name>Synaptosome</name>
                <parent>0</parent>
                <details>Central nervous system excitatiory synapse from a Munc13-1/2 double homozygous knockout mouse (Munc13 -/- -/-)</details>
                <natural_source database="NCBI">
                    <organism ncbi="10090">Mus musculus</organism>
                    <strain>C57 B6/N</strain>
                    <organ>brain</organ>
                    <tissue>hippocampus</tissue>
                    <organelle>excitatory synapse</organelle>
                </natural_source>
            </organelle_or_cellular_component_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">
                    <concentration units="mg/mL">0.4</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <component>
                            <concentration units="mM">300.0</concentration>
                            <formula>HBM</formula>
                            <name>Hepes-buffered medium</name>
                        </component>
                        <details>140 mM NaCl, 5 mM KCl, 5mM NaHCO3, 1.2 mM NaH2PO4-H2O, 1 mM MgCl26-H2O, 10 mM Glucose, 10 mM Hepes, 1.2 mM CaCl2</details>
                    </buffer>
                    <grid>
                        <model>Quantifoil R2/1</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>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <details>Portable manual plunger made at Max Planck Institute of Biochemistry. </details>
                    </vitrification>
                    <details>Synaptosomal fraction (P2) was obtained from DIV 28-30 hippocampal organotypic slices.
These hippocampal organotypic slices were obtained from E18 mice.</details>
                    <fiducial_markers_list>
                        <fiducial_marker>
                            <manufacturer>Aurion</manufacturer>
                            <diameter units="nanometer">10</diameter>
                        </fiducial_marker>
                    </fiducial_markers_list>
                    <cryo_protectant>None</cryo_protectant>
                    <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">0.5</nominal_defocus_min>
                    <nominal_defocus_max units="µm">1.0</nominal_defocus_max>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <basic/>
                    </alignment_procedure>
                    <specialist_optics>
                        <phase_plate>VOLTA PHASE PLATE</phase_plate>
                        <energy_filter>
                            <slit_width units="eV">20</slit_width>
                        </energy_filter>
                    </specialist_optics>
                    <software_list>
                        <software>
                            <name>SerialEM</name>
                        </software>
                    </software_list>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <average_electron_dose_per_image units="e/Å^2">1.5</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>BACK PROJECTION</algorithm>
                    <number_images_used>60</number_images_used>
                </final_reconstruction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="1377895">
        <file>emd_16085.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>928</col>
            <row>928</row>
            <sec>400</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>-46</sec>
        </origin>
        <spacing>
            <x>928</x>
            <y>928</y>
            <z>400</z>
        </spacing>
        <cell>
            <a units="Å">16295.68</a>
            <b units="Å">16295.68</b>
            <c units="Å">7024.0</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>-15000.019000000000233</minimum>
            <maximum>15000.019000000000233</maximum>
            <average>680.202300000000037</average>
            <std>563.933300000000031</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">17.56</x>
            <y units="Å">17.56</y>
            <z units="Å">17.56</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-16085::::</label>
        <annotation_details>Synapse Munc13 DKO 102 (id: m13_dko_102)</annotation_details>
    </map>
</emd>
