<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_8/emdb.xsd" emdb_id="EMD-10626" version="3.0.1.8">
    <admin>
        <current_status>
            <date>2020-03-11</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2020-01-20</deposition>
            <header_release>2020-02-19</header_release>
            <map_release>2020-03-11</map_release>
            <update>2020-03-11</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Wellcome Trust</funding_body>
                <code>WT100237</code>
                <country>United Kingdom</country>
            </grant_reference>
        </grant_support>
        <title>Negative stain map of CoREST complex (LSD1:RCOR1:HDAC1)</title>
        <authors_list>
            <author>Song Y</author>
            <author>Fairall L</author>
            <author>Ragan TJ</author>
            <author>Savva CG</author>
            <author>Saleh A</author>
            <author>Morone N</author>
            <author>Schwabe JWR</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Song Y</author>
                    <author order="2">Dagil L</author>
                    <author order="3">Fairall L</author>
                    <author order="4">Robertson N</author>
                    <author order="5">Wu M</author>
                    <author order="6">Ragan TJ</author>
                    <author order="7">Savva CG</author>
                    <author order="8">Saleh A</author>
                    <author order="9">Morone N</author>
                    <author order="10">Kunze MBA</author>
                    <author order="11">Jamieson AG</author>
                    <author order="12">Cole PA</author>
                    <author order="13">Hansen DF</author>
                    <author order="14">Schwabe JWR</author>
                    <title>Mechanism of Crosstalk between the LSD1 Demethylase and HDAC1 Deacetylase in the CoREST Complex.</title>
                    <journal_abbreviation>Cell Rep</journal_abbreviation>
                    <country>US</country>
                    <volume>30</volume>
                    <first_page>2699</first_page>
                    <last_page>2711.e8</last_page>
                    <year>2020</year>
                    <external_references type="PUBMED">32101746</external_references>
                    <external_references type="DOI">doi:10.1016/j.celrep.2020.01.091</external_references>
                    <external_references type="ISSN">2211-1247</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-10626</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Ternary complex of RCOR1 with the demethylase LSD1 and the deacetylase HDAC1</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Ternary complex of RCOR1 with the demethylase LSD1 and the deacetylase HDAC1</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
                    <recombinant_cell>HEK293F</recombinant_cell>
                    <recombinant_plasmid>pcDNA3</recombinant_plasmid>
                </recombinant_expression>
                <molecular_weight>
                    <theoretical units="MDa">0.21</theoretical>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>singleParticle</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <concentration units="mg/mL">0.01</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <component>
                            <concentration units="mM">25.0</concentration>
                            <formula>Tris</formula>
                            <name>Tris</name>
                        </component>
                        <component>
                            <concentration units="mM">50.0</concentration>
                            <formula>KCl</formula>
                            <name>potassium chloride</name>
                        </component>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <material>Uranyl Acetate</material>
                        <details>5 ul of 0.01 mg/ml of the CoREST ternary complex was applied onto the grid and the excess liquid was blotted after 1 minute incubation. 2% uranyl acetate was used to stain the sample.</details>
                    </staining>
                    <grid>
                        <model>C-flat</model>
                        <material>COPPER</material>
                        <mesh>400</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>CONTINUOUS</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                        </pretreatment>
                        <details>10 mA</details>
                    </grid>
                    <details>Sample was crosslinked with glutaraldehyde in 5-25% sucrose gradient and buffer exchanged to Tris buffer pH 7.5, 50 mM potassium acetate,0.5 mM TCEP.</details>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 2010F</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_cs units="mm">2.0</nominal_cs>
                    <nominal_defocus_min units="µm">0.5</nominal_defocus_min>
                    <nominal_defocus_max units="µm">2.0</nominal_defocus_max>
                    <nominal_magnification>60000.0</nominal_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">298.0</temperature_min>
                    </temperature>
                    <alignment_procedure>
                        <coma_free/>
                    </alignment_procedure>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <digitization_details>
                                <frames_per_image>1-48</frames_per_image>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>364</number_real_images>
                            <average_exposure_time units="s">1.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">30.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                </ctf_correction>
                <startup_model type_of_model="INSILICO MODEL">
                    <insilico_model>CryoSparc</insilico_model>
                </startup_model>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">17.5</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>3</version>
                        </software>
                    </software_list>
                    <number_images_used>2592</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing/>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing/>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <number_classes>4</number_classes>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="44958">
        <file>emd_10626.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>224</col>
            <row>224</row>
            <sec>224</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>224</x>
            <y>224</y>
            <z>224</z>
        </spacing>
        <cell>
            <a units="Å">430.08</a>
            <b units="Å">430.08</b>
            <c units="Å">430.08</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>-1.4343054</minimum>
            <maximum>3.8559563</maximum>
            <average>-0.022662451</average>
            <std>0.14412743</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.92</x>
            <y units="Å">1.92</y>
            <z units="Å">1.92</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.22</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-10626::::</label>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>4BKX</access_code>
                </initial_model>
                <initial_model>
                    <access_code>2VID</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
