<emd emdb_id="EMD-2991" 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>2015-04-29</deposition>
            <header_release>2015-06-17</header_release>
            <map_release>2015-07-15</map_release>
            <update>2015-11-25</update>
        </key_dates>
        <title>Electron cryo-tomography of polyQ seeded mutant huntingtin aggregates from PC12 cells inducibly expressing mHTTex1-GFP</title>
        <authors_list>
            <author>Tan Z</author>
            <author>Dai W</author>
            <author>van Erp TGM</author>
            <author>Overman J</author>
            <author>Demuro A</author>
            <author>Digman MA</author>
            <author>Hatami A</author>
            <author>Albay R</author>
            <author>Sontag EM</author>
            <author>Potkin KT</author>
            <author>Ling S</author>
            <author>Macciardi F</author>
            <author>Bunney WE</author>
            <author>Long JD</author>
            <author>Paulsen JS</author>
            <author>Ringman JM</author>
            <author>Parker I</author>
            <author>Glabe C</author>
            <author>Thompson LM</author>
            <author>Chiu W</author>
            <author>Potkin SG</author>
        </authors_list>
        <keywords>Huntington's disease, seeding, cerebrospinal fluid, mutant huntingtin aggregates, cell lysate</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Tan Z</author>
                    <author order="2">Dai W</author>
                    <author order="3">van Erp TGM</author>
                    <author order="4">Overman J</author>
                    <author order="5">Demuro A</author>
                    <author order="6">Digman MA</author>
                    <author order="7">Hatami A</author>
                    <author order="8">Albay R</author>
                    <author order="9">Sontag EM</author>
                    <author order="10">Potkin KT</author>
                    <author order="11">Ling S</author>
                    <author order="12">Macciardi F</author>
                    <author order="13">Bunney WE</author>
                    <author order="14">Long JD</author>
                    <author order="15">Paulsen JS</author>
                    <author order="16">Ringman JM</author>
                    <author order="17">Parker I</author>
                    <author order="18">Glabe C</author>
                    <author order="19">Thompson LM</author>
                    <author order="20">Chiu W</author>
                    <author order="21">Potkin SG</author>
                    <title>Huntington's disease cerebrospinal fluid seeds aggregation of mutant huntingtin</title>
                    <journal>Mol. Psychiatry</journal>
                    <volume>20</volume>
                    <first_page>1286</first_page>
                    <last_page>1293</last_page>
                    <year>2015</year>
                    <external_references type="PUBMED">26100538</external_references>
                    <external_references type="DOI">doi:10.1038/mp.2015.81</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>PolyQ seeded mutant huntingtin aggregates from PC12 cells inducibly expressing mHTTex1-GFP</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>PolyQ seeded mutant huntingtin aggregates from PC12 cells inducibly expressing mHTTex1-GFP</name>
                <details>This sample is synthetic polyQ (KKQ40KK) seeded mutant huntingtin aggregates from PC12 cell lysates. These PC12 cells inducibly express mHTTex1-GFP.</details>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name>mutant huntingtin aggregates</name>
                <details>This sample is synthetic polyQ oligomer (KKQ40QQ) seeded mutant huntingtin aggregates from PC12 cell lysates. These cells inducibly express mHTTex1-GFP.</details>
                <oligomeric_state>oligomers and fibrils</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <natural_source database="NCBI">
                    <organism ncbi="10116">Rattus norvegicus</organism>
                    <synonym_organism>Norway rat</synonym_organism>
                    <tissue>adrenal medulla</tissue>
                    <cell>pheochromocytoma</cell>
                    <cellular_location>cell lysate</cellular_location>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="10116">Rattus norvegicus</recombinant_organism>
                    <recombinant_cell>PC12 cells</recombinant_cell>
                    <recombinant_plasmid>pIND</recombinant_plasmid>
                </recombinant_expression>
            </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">
                    <grid>
                        <details>200 mesh gold grid with thin carbon support, glow discharged for 20 second</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <instrument>LEICA EM GP</instrument>
                        <method>Blot for 2 second before plunging</method>
                    </vitrification>
                </tomography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <tomography_microscopy microscopy_id="1">
                    <microscope>JEOL 2100</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_cs units="mm">2.0</nominal_cs>
                    <nominal_defocus_min units="&#181;m">6.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">8.0</nominal_defocus_max>
                    <nominal_magnification>15000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 100,000 times magnification</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2013-12-12</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <number_real_images>40</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">60</average_electron_dose_per_image>
                            <detector_distance>1200</detector_distance>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Gatan 626 70 degree</specimen_holder>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">-60</min_angle>
                            <max_angle units="deg">60</max_angle>
                            <angle_increment units="deg">3</angle_increment>
                        </axis1>
                    </tilt_series>
                </tomography_microscopy>
            </microscopy_list>
            <tomography_processing image_processing_id="1">
                <details>alignment and reconstruction were done using IMOD</details>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                        </software>
                    </software_list>
                    <details>Final map was reconstructed by back projection</details>
                    <number_images_used>40</number_images_used>
                </final_reconstruction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
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        <file>emd_2991.map.gz</file>
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            <space_group>1</space_group>
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            <row>636</row>
            <sec>122</sec>
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            <col>-190</col>
            <row>68</row>
            <sec>-10</sec>
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            <x>636</x>
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            <z>122</z>
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        <cell>
            <a units="&#8491;">22308.0</a>
            <b units="&#8491;">18189.6</b>
            <c units="&#8491;">3489.2</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>-1425.988159179999911</minimum>
            <maximum>1030.745117189999974</maximum>
            <average>19.078897479999998</average>
            <std>48.196453089999999</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">28.6</x>
            <y units="&#8491;">28.599998</y>
            <z units="&#8491;">28.6</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>60.0</level>
                <source>EMDB</source>
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        <annotation_details>Reconstruction of polyQ seeded mutant huntingtin aggregates from PC12 cells inducibly expressing mHTTex1-GFP</annotation_details>
        <details>::::EMDATABANK.org::::EMD-2991::::</details>
    </map>
</emd>