<?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-46757">
    <admin>
        <current_status>
            <date>2025-05-14</date>
            <code>REL</code>
            <processing_site>RCSB</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>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2024-08-27</deposition>
            <header_release>2025-03-05</header_release>
            <map_release>2025-03-05</map_release>
            <update>2025-05-14</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Science Foundation (NSF, United States)</funding_body>
                <code>MCB-2046180</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Human Frontier Science Program (HFSP)</funding_body>
                <code>LT001044/2017</code>
                <country>France</country>
            </grant_reference>
        </grant_support>
        <title>Cryo-electron tomography of amorphous alpha-synuclein aggregates with embedded membranes and a lipid droplet</title>
        <authors_list>
            <author ORCID="0000-0002-1750-4550">Jaber N</author>
            <author ORCID="0000-0003-3032-3399">Dai W</author>
        </authors_list>
        <keywords>intrinsic disorder, aggregate, amorphous, phase separation, neurodegeneration, membrane binding, neurotransmitter regulation, EXOCYTOSIS</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Eubanks E</author>
                    <author order="2">VanderSleen K</author>
                    <author order="3">Mody J</author>
                    <author order="4">Patel N</author>
                    <author order="5">Sacks B</author>
                    <author order="6">Farahani MD</author>
                    <author order="7">Wang J</author>
                    <author order="8">Elliott J</author>
                    <author order="9">Jaber N</author>
                    <author order="10">Akcimen F</author>
                    <author order="11">Bandres-Ciga S</author>
                    <author order="12">Helweh F</author>
                    <author order="13">Liu J</author>
                    <author order="14">Archakam S</author>
                    <author order="15">Kimelman R</author>
                    <author order="16">Sharma B</author>
                    <author order="17">Socha P</author>
                    <author order="18">Guntur A</author>
                    <author order="19">Huang Y</author>
                    <author order="20">Ramalingam N</author>
                    <author order="21">Guadagno E</author>
                    <author order="22">Bartels T</author>
                    <author order="23">Dettmer U</author>
                    <author order="24">Mouradian MM</author>
                    <author order="25">Bahrami AH</author>
                    <author order="26">Dai W</author>
                    <author order="27">Baum J</author>
                    <author order="28">Shi Z</author>
                    <author order="29">Hardy J</author>
                    <author order="30">Kara E</author>
                    <title>Increased burden of rare risk variants across gene expression networks predisposes to sporadic Parkinson's disease.</title>
                    <journal_abbreviation>Cell Rep</journal_abbreviation>
                    <country>US</country>
                    <volume>44</volume>
                    <first_page>115636</first_page>
                    <last_page>115636</last_page>
                    <year>2025</year>
                    <external_references type="PUBMED">40317721</external_references>
                    <external_references type="DOI">doi:10.1016/j.celrep.2025.115636</external_references>
                    <external_references type="ISSN">2211-1247</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Cell lysate from 3k M17D neuroblastoma cell line</name>
        <supramolecule_list>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name>Cell lysate from 3k M17D neuroblastoma cell line</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </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">
                    <buffer>
                        <ph>7.4</ph>
                        <component>
                            <concentration units="mM">20.0</concentration>
                            <formula>Tris-Base</formula>
                            <name>Tris-Base</name>
                        </component>
                        <component>
                            <concentration units="mM">10.0</concentration>
                            <formula>NaCl</formula>
                            <name>sodium chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">3.0</concentration>
                            <formula>MgCl2</formula>
                            <name>magnesium chloride</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R2/2</model>
                        <material>COPPER</material>
                        <mesh>200</mesh>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <time units="s">25</time>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">95</chamber_humidity>
                        <chamber_temperature units="K">293.15</chamber_temperature>
                        <instrument>LEICA EM GP</instrument>
                        <details>Blot time: 6 seconds. </details>
                    </vitrification>
                    <fiducial_markers_list>
                        <fiducial_marker>
                            <manufacturer>EMS</manufacturer>
                            <diameter units="nanometer">6</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 TALOS ARCTICA</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_defocus_min units="µm">8.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">10.0</nominal_defocus_max>
                    <nominal_magnification>31000.0</nominal_magnification>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <basic/>
                    </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 K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <number_real_images>41</number_real_images>
                            <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>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                        </software>
                    </software_list>
                    <number_images_used>41</number_images_used>
                </final_reconstruction>
                <ctf_correction>
                    <type>NONE</type>
                </ctf_correction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="536952">
        <file>emd_46757.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>927</col>
            <row>959</row>
            <sec>151</sec>
        </dimensions>
        <origin>
            <col>-16</col>
            <row>16</row>
            <sec>84</sec>
        </origin>
        <spacing>
            <x>927</x>
            <y>959</y>
            <z>151</z>
        </spacing>
        <cell>
            <a units="Å">15944.4</a>
            <b units="Å">16494.8</b>
            <c units="Å">2597.2002</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>0.0</minimum>
            <maximum>1.0</maximum>
            <average>0.49734125</average>
            <std>0.28606188</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">17.2</x>
            <y units="Å">17.2</y>
            <z units="Å">17.2</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-46757::::</label>
        <annotation_details>Amorphous alpha-synuclein aggregate with embedded membranes, including a lipid droplet.</annotation_details>
    </map>
</emd>
