<?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-53597">
    <admin>
        <current_status>
            <date>2026-02-04</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <revision_history>
            <revision version="1.0" date="2026-02-04">
                <change_list>
                    <metadata>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </metadata>
                    <additional_map part="1">
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </additional_map>
                    <fsc>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </fsc>
                    <half_map part="1">
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </half_map>
                    <half_map part="2">
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </half_map>
                    <image>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </image>
                    <mask part="1">
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </mask>
                    <primary_map>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </primary_map>
                </change_list>
            </revision>
        </revision_history>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2025-05-10</deposition>
            <header_release>2026-02-04</header_release>
            <map_release>2026-02-04</map_release>
            <update>2026-02-04</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Medical Research Council (MRC, United Kingdom)</funding_body>
                <country>United Kingdom</country>
            </grant_reference>
        </grant_support>
        <title>Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing.</title>
        <authors_list>
            <author>Sundaramoorthy R</author>
            <author>Hughes A</author>
            <author>Owen-hughes TA</author>
        </authors_list>
        <keywords>Nucleosome, Remodelling enzyme, GENE REGULATION</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Hughes AL</author>
                    <author ORCID="0000-0003-4895-0980" order="2">Sundaramoorthy R</author>
                    <author ORCID="0000-0002-0618-8185" order="3">Owen-Hughes T</author>
                    <title>Structural characterisation of chromatin remodelling intermediates supports linker DNA-dependent product inhibition as a mechanism for nucleosome spacing.</title>
                    <journal_abbreviation>Elife</journal_abbreviation>
                    <country>US</country>
                    <volume>14</volume>
                    <year>2025</year>
                    <external_references type="PUBMED">41439750</external_references>
                    <external_references type="DOI">doi:10.7554/eLife.52513</external_references>
                    <external_references type="ISSN">2050-084X</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <other_db_list>
            <db_reference>
                <db_name>EMDB</db_name>
                <accession_id>EMD-53597</accession_id>
                <content_type>associated EM volume</content_type>
            </db_reference>
        </other_db_list>
    </crossreferences>
    <sample>
        <name>Nucleosome-Chd1 complex</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Nucleosome-Chd1 complex</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>3</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <details>Chd1 remodeller bound to Nucleosome</details>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.4</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">1.5</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <component>
                            <concentration units="mM">120.0</concentration>
                            <formula>Nacl</formula>
                            <name>Sodium chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">20.0</concentration>
                            <formula>Hepes</formula>
                            <name>Hepes</name>
                        </component>
                        <details>20mM Hepes, 120mM Nacl</details>
                    </buffer>
                    <grid>
                        <model>Quantifoil R2/1</model>
                        <material>COPPER/RHODIUM</material>
                        <mesh>400</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <time units="s">60</time>
                            <atmosphere>AIR</atmosphere>
                            <pressure units="kPa">0.0001</pressure>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">277</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <details>Vitrified carried out in climate chamber with 100% humidity. </details>
                    </vitrification>
                    <details>Purified Nucleosome-Chd1 complex.</details>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>TFS 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>
                    <c2_aperture_diameter units="µm">50.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">1.8</nominal_defocus_min>
                    <calibrated_defocus_min units="µm">1.8</calibrated_defocus_min>
                    <nominal_defocus_max units="µm">3.2</nominal_defocus_max>
                    <calibrated_defocus_max units="µm">3.2</calibrated_defocus_max>
                    <nominal_magnification>81000.0</nominal_magnification>
                    <calibrated_magnification>81000.0</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">77.0</temperature_min>
                        <temperature_max units="K">77.0</temperature_max>
                    </temperature>
                    <alignment_procedure>
                        <coma_free/>
                    </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 K3 BIOQUANTUM (6k x 4k)</film_or_detector_model>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>2562</number_real_images>
                            <average_exposure_time units="s">10.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">46.0</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>
                <particle_selection>
                    <number_selected>2700000</number_selected>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>4.5.3</version>
                        </software>
                    </software_list>
                    <type>PHASE FLIPPING ONLY</type>
                </ctf_correction>
                <startup_model type_of_model="PDB ENTRY">
                    <pdb_model>
                        <pdb_id>3LZ0</pdb_id>
                    </pdb_model>
                </startup_model>
                <final_reconstruction>
                    <number_classes_used>1</number_classes_used>
                    <algorithm>FOURIER SPACE</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">4.27</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>4.5.3</version>
                        </software>
                    </software_list>
                    <number_images_used>129000</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>ANGULAR RECONSTITUTION</type>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>4.5.3</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>ANGULAR RECONSTITUTION</type>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>4.5.3</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <number_classes>4</number_classes>
                    <average_number_members_per_class>100000.0</average_number_members_per_class>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>4.5.3</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="702465">
        <file>emd_53597.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>560</col>
            <row>560</row>
            <sec>560</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>560</x>
            <y>560</y>
            <z>560</z>
        </spacing>
        <cell>
            <a units="Å">308.0</a>
            <b units="Å">308.0</b>
            <c units="Å">308.0</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>-0.004127448</minimum>
            <maximum>1.8975159</maximum>
            <average>0.0015620502</average>
            <std>0.030215451</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">0.55</x>
            <y units="Å">0.55</y>
            <z units="Å">0.55</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.02</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-53597::::</label>
        <annotation_details>Main Map</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3LZ0</access_code>
                    <chain>
                        <source_name>PDB</source_name>
                        <initial_model_type>experimental model</initial_model_type>
                    </chain>
                </initial_model>
                <initial_model>
                    <access_code>6FTX</access_code>
                    <chain>
                        <source_name>PDB</source_name>
                        <initial_model_type>experimental model</initial_model_type>
                    </chain>
                </initial_model>
                <initial_model>
                    <access_code>7TN2</access_code>
                    <chain>
                        <source_name>PDB</source_name>
                        <initial_model_type>experimental model</initial_model_type>
                    </chain>
                </initial_model>
                <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
                <target_criteria>cross-correlation</target_criteria>
                <refinement_space>REAL</refinement_space>
                <overall_bvalue>180.0</overall_bvalue>
            </modelling>
        </modelling_list>
        <segmentation_list>
            <segmentation>
                <file>emd_53597_msk_1.map</file>
            </segmentation>
        </segmentation_list>
        <additional_map_list>
            <additional_map format="CCP4" size_kbytes="702465">
                <file>emd_53597_additional_1.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>560</col>
                    <row>560</row>
                    <sec>560</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>560</x>
                    <y>560</y>
                    <z>560</z>
                </spacing>
                <cell>
                    <a units="Å">308.0</a>
                    <b units="Å">308.0</b>
                    <c units="Å">308.0</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>-0.018916218</minimum>
                    <maximum>0.048982687</maximum>
                    <average>0.000082579514</average>
                    <std>0.0018827545</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">0.55</x>
                    <y units="Å">0.55</y>
                    <z units="Å">0.55</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-53597::::</label>
                <annotation_details>Non sharpened Main Map</annotation_details>
            </additional_map>
        </additional_map_list>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="702465">
                <file>emd_53597_half_map_2.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>560</col>
                    <row>560</row>
                    <sec>560</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>560</x>
                    <y>560</y>
                    <z>560</z>
                </spacing>
                <cell>
                    <a units="Å">308.0</a>
                    <b units="Å">308.0</b>
                    <c units="Å">308.0</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>-0.5224846</minimum>
                    <maximum>0.46912897</maximum>
                    <average>0.00009894266</average>
                    <std>0.051468633</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">0.55</x>
                    <y units="Å">0.55</y>
                    <z units="Å">0.55</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-53597::::</label>
                <annotation_details>Half Map</annotation_details>
            </half_map>
            <half_map format="CCP4" size_kbytes="702465">
                <file>emd_53597_half_map_1.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>560</col>
                    <row>560</row>
                    <sec>560</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>560</x>
                    <y>560</y>
                    <z>560</z>
                </spacing>
                <cell>
                    <a units="Å">308.0</a>
                    <b units="Å">308.0</b>
                    <c units="Å">308.0</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>-0.45003897</minimum>
                    <maximum>0.45734474</maximum>
                    <average>0.00009956525</average>
                    <std>0.051421486</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">0.55</x>
                    <y units="Å">0.55</y>
                    <z units="Å">0.55</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-53597::::</label>
                <annotation_details>Half Map</annotation_details>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
