<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-17154">
    <admin>
        <current_status>
            <date>2023-07-26</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2023-04-19</deposition>
            <header_release>2023-05-24</header_release>
            <map_release>2023-05-24</map_release>
            <update>2023-07-26</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>European Research Council (ERC)</funding_body>
                <code>884331</code>
                <country>European Union</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Human Frontier Science Program (HFSP)</funding_body>
                <code>LT000646/2018-L5</code>
                <country>France</country>
            </grant_reference>
        </grant_support>
        <title>Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8  (consensus and constituent map 1)</title>
        <authors_list>
            <author>Stoos L</author>
            <author>Michael AK</author>
            <author>Kempf G</author>
            <author>Cavadini S</author>
            <author>Thoma NH</author>
        </authors_list>
        <keywords>E-box, transcription factor, circadian clock, GENE REGULATION</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0002-6080-839X" order="1">Michael AK</author>
                    <author order="2">Stoos L</author>
                    <author order="3">Crosby P</author>
                    <author ORCID="0000-0002-0256-1982" order="4">Eggers N</author>
                    <author order="5">Nie XY</author>
                    <author ORCID="0000-0002-0645-6848" order="6">Makasheva K</author>
                    <author ORCID="0000-0003-4677-3300" order="7">Minnich M</author>
                    <author order="8">Healy KL</author>
                    <author ORCID="0000-0002-4149-0478" order="9">Weiss J</author>
                    <author order="10">Kempf G</author>
                    <author order="11">Cavadini S</author>
                    <author order="12">Kater L</author>
                    <author order="13">Seebacher J</author>
                    <author order="14">Vecchia L</author>
                    <author order="15">Chakraborty D</author>
                    <author ORCID="0000-0002-5270-4347" order="16">Isbel L</author>
                    <author order="17">Grand RS</author>
                    <author order="18">Andersch F</author>
                    <author order="19">Fribourgh JL</author>
                    <author order="20">Schubeler D</author>
                    <author ORCID="0000-0001-8810-6835" order="21">Zuber J</author>
                    <author ORCID="0000-0003-1927-0900" order="22">Liu AC</author>
                    <author ORCID="0000-0001-7186-0372" order="23">Becker PB</author>
                    <author ORCID="0000-0002-2991-3044" order="24">Fierz B</author>
                    <author ORCID="0000-0002-4677-2861" order="25">Partch CL</author>
                    <author ORCID="0000-0002-7682-0967" order="26">Menet JS</author>
                    <author ORCID="0000-0003-2685-906X" order="27">Thoma NH</author>
                    <title>Cooperation between bHLH transcription factors and histones for DNA access.</title>
                    <journal_abbreviation>Nature</journal_abbreviation>
                    <country>UK</country>
                    <volume>619</volume>
                    <first_page>385</first_page>
                    <last_page>393</last_page>
                    <year>2023</year>
                    <external_references type="PUBMED">37407816</external_references>
                    <external_references type="DOI">doi:10.1038/s41586-023-06282-3</external_references>
                    <external_references type="ISSN">1476-4687</external_references>
                    <external_references type="CSD">0006</external_references>
                    <external_references type="ASTM">NATUAS</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-17157</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>CLOCK-BMAL1 bound to a nucleosome SHL+5.8 (composite map)</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-17158</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>CLOCK-BMAL1 bound to a nucleosome SHL+5.8 (focused map)</details>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>CLOCK-BMAL1 bound to a nucleosome SHL+5.8</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>CLOCK-BMAL1 bound to a nucleosome SHL+5.8</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
            </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">
                    <buffer>
                        <ph>7.2</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_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">2.5</nominal_defocus_max>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI FALCON IV (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">50.0</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>
                <startup_model type_of_model="OTHER"/>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">3.6</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <number_images_used>25483</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>OTHER</type>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>OTHER</type>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
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        <file>emd_17154.map.gz</file>
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            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
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            <col>360</col>
            <row>360</row>
            <sec>360</sec>
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        <spacing>
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            <y>360</y>
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        <cell>
            <a units="Å">304.2</a>
            <b units="Å">304.2</b>
            <c units="Å">304.2</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>
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        <statistics>
            <minimum>-0.29923418</minimum>
            <maximum>0.82261384</maximum>
            <average>-0.0010086528</average>
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            <x units="Å">0.845</x>
            <y units="Å">0.845</y>
            <z units="Å">0.845</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0868</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-17154::::</label>
        <annotation_details>Full map.</annotation_details>
    </map>
    <interpretation>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="186625">
                <file>emd_17154_half_map_2.map.gz</file>
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                    <space_group>1</space_group>
                </symmetry>
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                <dimensions>
                    <col>360</col>
                    <row>360</row>
                    <sec>360</sec>
                </dimensions>
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                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
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                    <x>360</x>
                    <y>360</y>
                    <z>360</z>
                </spacing>
                <cell>
                    <a units="Å">304.2</a>
                    <b units="Å">304.2</b>
                    <c units="Å">304.2</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>
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                <statistics>
                    <minimum>-2.1866217</minimum>
                    <maximum>1.9755872</maximum>
                    <average>0.0008376995</average>
                    <std>0.24512735</std>
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                    <y units="Å">0.845</y>
                    <z units="Å">0.845</z>
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                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-17154::::</label>
                <annotation_details>Half-map B.</annotation_details>
            </half_map>
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                <file>emd_17154_half_map_1.map.gz</file>
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                </symmetry>
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                    <b units="Å">304.2</b>
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                    <beta units="deg">90.0</beta>
                    <gamma units="deg">90.0</gamma>
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                    <fast>X</fast>
                    <medium>Y</medium>
                    <slow>Z</slow>
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                    <minimum>-1.8958611</minimum>
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                    <average>0.000845138</average>
                    <std>0.24332131</std>
                </statistics>
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                    <y units="Å">0.845</y>
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                        <source>AUTHOR</source>
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                <label>::::EMDATABANK.org::::EMD-17154::::</label>
                <annotation_details>Half-map A.</annotation_details>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
