<?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-20391" version="3.0.1.8">
    <admin>
        <current_status>
            <date>2020-03-04</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-07-01</deposition>
            <header_release>2019-08-21</header_release>
            <map_release>2019-08-21</map_release>
            <update>2020-03-04</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences</funding_body>
                <code>R01-67167</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases</funding_body>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>CryoEM structure of mouse mediator subunit one deletion</title>
        <authors_list>
            <author>Asturias F</author>
            <author>Zhao H</author>
            <author>Young N</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">El Khattabi L</author>
                    <author order="2">Zhao H</author>
                    <author order="3">Kalchschmidt J</author>
                    <author order="4">Young N</author>
                    <author order="5">Jung S</author>
                    <author order="6">Van Blerkom P</author>
                    <author order="7">Kieffer-Kwon P</author>
                    <author order="8">Kieffer-Kwon KR</author>
                    <author order="9">Park S</author>
                    <author order="10">Wang X</author>
                    <author order="11">Krebs J</author>
                    <author order="12">Tripathi S</author>
                    <author order="13">Sakabe N</author>
                    <author order="14">Sobreira DR</author>
                    <author order="15">Huang SC</author>
                    <author order="16">Rao SSP</author>
                    <author order="17">Pruett N</author>
                    <author order="18">Chauss D</author>
                    <author order="19">Sadler E</author>
                    <author order="20">Lopez A</author>
                    <author order="21">Nobrega MA</author>
                    <author order="22">Aiden EL</author>
                    <author order="23">Asturias FJ</author>
                    <author order="24">Casellas R</author>
                    <title>A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers.</title>
                    <journal_abbreviation>Cell</journal_abbreviation>
                    <volume>178</volume>
                    <first_page>1145</first_page>
                    <last_page>1158.e20</last_page>
                    <year>2019</year>
                    <external_references type="PUBMED">31402173</external_references>
                    <external_references type="DOI">doi:10.1016/j.cell.2019.07.011</external_references>
                    <external_references type="ISSN">1097-4172</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-20391</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>mouse mediator subunit</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>mouse mediator subunit</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="10090">Mus musculus</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="10090">Mus musculus</recombinant_organism>
                    <recombinant_cell>CH12 B cells</recombinant_cell>
                </recombinant_expression>
                <molecular_weight>
                    <theoretical units="MDa">1.0</theoretical>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <other_macromolecule macromolecule_id="1">
                <name>mouse mediator subunit</name>
                <natural_source database="NCBI">
                    <organism ncbi="10090">Mus musculus</organism>
                </natural_source>
                <sequence>
                    <string>MAPVQLDNHQLIPPGGGGGSSGGGGSSSGSASAPAPPPPAAAVAAAAAAAASPGYRLSTL
IEFLLHRAYSELMVLTDLLPRKSDVERKIEIVQFASRTRQLFVRLLALVKWANDAGKVEK
CAMISSFLDQQAILFVDTADRLASLARDALVHARLPSFAIPYAIDVLTTGSYPRLPTCIR
DKIIPPDPITKIEKQATLHQLNQILRHRLVTTDLPPQLANLTVANGRVKFRVEGEFEATL
TVMGDDPEVPWRLLKLEILVEDKETGDGRALVHSMQIDFIHQLVQSRLFADEKPLQDMYN
CLHCFCLSLQLEVLHSQTLMLIRERWGDLVQVERYHAGKSLSLSVWNQQVLGRKTGTASV
HKVTIKIDENDVSKPLQIFHDPPLPASDSKLVERAMKIDHLSIEKLLIDSVHARAHQRLQ
ELKAILRSFNANESSSIETALPALIVPILEPCGNSECLHIFVDLHSGMFQLMLYGLDPAT
LEDMEKSLNDDMKRIIPWIQQLKFWLGQQRCKQSIKHLPTITTETLQLANYSTHPIGSLS
KNKLFIKLTRLPQYYIVVEMLEVPNKPTQLSYNYYFMSVSTADREDSPVMALLLQQFKDN
IQDLMSYTKTGKQTRTGTKHKLSDDPCPIDSKKAKRSGEMCAFNKVLAHFVAMCDTNMPF
VGLRLELSNLEIPHQGVQVEGDGFNHAIRLLKIPPCKGISEETQKALDRSLLDCTFRLQG
RNNRTWVAELVFANCPLNGTSTREQGPSRHVYLTYENLLSEPVGGRKVVEMFLNDWSSIA
RLYECVLEFARSLPEIPAHLNIFSEVRVYNYRKLILCYGTTKGSSISIQWNSIHQKFHIA
LGTVGPNSGCSNCHNTILHQLQEMFNKTPNVVQLLQVLFDTQAPLNAINKLPTVPMLGLT
QRTNTAYQCFSILPQSSTHIRLAFRNMYCIDIYCRSRGVVAIRDGAYSLFDNSKLVEGFY
PAPGLKTFLNMFVDSNQDARRRSVNEDDNPPSPIGGDMMDSLISQLQPPQQQPFPKQPGT
SGAYPLTSPPTSYHSTVNQSPSMMHTQSPGNLHAASSPSGALRAPSPASFVPTPPPSSHG
ISIGPGASFASPHGTLDPSSPYTMVSPSGRAGNWPGSPQVSGPSPATRLPGMSPANPSLH
SPVPDVSHSPRAGTSSQTMPTNMPPPRKLPQRSWAASIPTILTHSALNILLLPSPTPGLV
PGLAGSYLCSPLERFLGSVIMRRHLQRIIQQETLQLINSNEPGVIMFKTDALKCRVALSP
KTNQTLQLKVTPENAGQWKPDELQVLEKFFETRVAGPPFKANTLIAFTKLLGAPTHILRD
CVHIMKLELFPDQATQLKWNVQFCLTIPPSAPPIAPPGTPAVVLKSKMLFFLQLTQKTSV
PPQEPVSIIVPIIYDMASGTTQQADIPRQQNSSVAAPMMVSNILKRFAEMNPPRQGECTI
FAAVRDLMANLTLPPGGRP</string>
                </sequence>
                <classification>other</classification>
            </other_macromolecule>
        </macromolecule_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">0.5</concentration>
                    <buffer>
                        <ph>7.9</ph>
                        <component>
                            <concentration units="mM">50.0</concentration>
                            <formula>C8H18N2O4S</formula>
                            <name>HEPES</name>
                        </component>
                    </buffer>
                    <grid>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>CONTINUOUS</film_topology>
                            <film_thickness units="nm">3.0</film_thickness>
                        </support_film>
                        <details>unspecified</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">273</chamber_temperature>
                        <instrument>FEI VITROBOT MARK II</instrument>
                        <details></details>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI 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>
                    <c2_aperture_diameter units="µm">70.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">1.2</nominal_defocus_min>
                    <calibrated_defocus_min units="µm">1.2</calibrated_defocus_min>
                    <nominal_defocus_max units="µm">5.0</nominal_defocus_max>
                    <calibrated_defocus_max units="µm">5.0</calibrated_defocus_max>
                    <nominal_magnification>22000.0</nominal_magnification>
                    <calibrated_magnification>22000.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <temperature>
                        <temperature_min units="K">70.0</temperature_min>
                        <temperature_max units="K">70.0</temperature_max>
                    </temperature>
                    <alignment_procedure>
                        <coma_free/>
                    </alignment_procedure>
                    <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>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">3838</width>
                                    <height units="pixel">3710</height>
                                </dimensions>
                                <frames_per_image>28-32</frames_per_image>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>4339</number_real_images>
                            <average_exposure_time units="s">10.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">39.7</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>
                <particle_selection>
                    <number_selected>18688</number_selected>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>CTFFIND</name>
                        </software>
                    </software_list>
                </ctf_correction>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">8.28</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                        </software>
                    </software_list>
                    <number_images_used>18688</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>RANDOM ASSIGNMENT</type>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>RANDOM ASSIGNMENT</type>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <number_classes>200</number_classes>
                    <average_number_members_per_class>700</average_number_members_per_class>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="186625">
        <file>emd_20391.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>360</col>
            <row>360</row>
            <sec>360</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>360</x>
            <y>360</y>
            <z>360</z>
        </spacing>
        <cell>
            <a units="Å">661.4316</a>
            <b units="Å">661.4316</b>
            <c units="Å">661.4316</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>-1.3210069</minimum>
            <maximum>2.486549</maximum>
            <average>0.0016588357</average>
            <std>0.05789689</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.83731</x>
            <y units="Å">1.83731</y>
            <z units="Å">1.83731</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.28</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-20391::::</label>
        <annotation_details>CryoEM structure of mouse mediator subunit one delection</annotation_details>
    </map>
</emd>
