<?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-47844">
    <admin>
        <current_status>
            <date>2026-03-18</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <revision_history>
            <revision version="1.0" date="2026-03-18">
                <change_list>
                    <metadata>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </metadata>
                    <image>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </image>
                    <primary_map>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </primary_map>
                </change_list>
            </revision>
        </revision_history>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2024-11-11</deposition>
            <header_release>2026-03-18</header_release>
            <map_release>2026-03-18</map_release>
            <update>2026-03-18</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Montaged cryo-ET map of individual particle 3D reconstructions of ~2 kb negatively supercoiled plasmids (delta Lk centered on -15) under near physiological salt condition (40 mM K+, 5 mM Mg2+)</title>
        <authors_list>
            <author ORCID="0000-0001-9735-8970">Zhang M</author>
            <author ORCID="0000-0002-2970-0073">Bustamante C</author>
        </authors_list>
        <keywords>DNA Supercoiling, Transcription regulation, Cryo-Electron Tomography (cryo-ET), Topological Domains, DNA</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Zhang M</author>
                    <author order="2">Bustamante C</author>
                    <title>Interplay Between DNA Supercoiling and RNA Polymerase Localization at Plectoneme Apices Modulate Transcription Dynamics</title>
                    <journal_abbreviation>To Be Published</journal_abbreviation>
                    <external_references type="CSD">0353</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <other_db_list>
            <db_reference>
                <db_name>EMDB</db_name>
                <accession_id>EMD-47844</accession_id>
                <content_type>associated EM volume</content_type>
            </db_reference>
        </other_db_list>
    </crossreferences>
    <sample>
        <name>2 kb negatively supercoiled pUC19 plasmids containing a T7A1-U promoter</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>2 kb negatively supercoiled pUC19 plasmids containing a T7A1-U promoter</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                    <details>pUC19 plasmid</details>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>tomography</method>
            <aggregation_state>filament</aggregation_state>
            <specimen_preparation_list>
                <tomography_preparation preparation_id="1">
                    <buffer>
                        <ph>7.4</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">95</chamber_humidity>
                        <chamber_temperature units="K">288</chamber_temperature>
                        <instrument>LEICA EM GP</instrument>
                    </vitrification>
                    <sectioning>
                        <other_sectioning>NO SECTIONING</other_sectioning>
                    </sectioning>
                </tomography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <tomography_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>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">2.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">4.0</nominal_defocus_max>
                    <nominal_magnification>53000.0</nominal_magnification>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K3 (6k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">130.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </tomography_microscopy>
            </microscopy_list>
            <tomography_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <software_list>
                        <software>
                            <name>EMAN2</name>
                        </software>
                        <software>
                            <name>SPIDER</name>
                        </software>
                    </software_list>
                    <number_images_used>35</number_images_used>
                </final_reconstruction>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>EMAN2</name>
                        </software>
                    </software_list>
                    <type>PHASE FLIPPING ONLY</type>
                </ctf_correction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="960001">
        <file>emd_47844.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>1200</col>
            <row>1000</row>
            <sec>200</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>1200</x>
            <y>1000</y>
            <z>200</z>
        </spacing>
        <cell>
            <a units="Å">14027.999</a>
            <b units="Å">11690.0</b>
            <c units="Å">2338.0</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>-0.5162568</minimum>
            <maximum>4.5810475</maximum>
            <average>0.0009016721</average>
            <std>0.031435337</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">11.69</x>
            <y units="Å">11.69</y>
            <z units="Å">11.69</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-47844::::</label>
        <annotation_details>Montaged cryo-ET map of individual particle 3D reconstructions of ~2 kb negatively supercoiled plasmids (delta Lk centered on -15) under near physiological salt condition (40 mM K , 5 mM Mg2 )</annotation_details>
    </map>
</emd>
