<?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_9_1/emdb.xsd" version="3.0.9.1" emdb_id="EMD-37413">
    <admin>
        <current_status>
            <date>2024-01-03</date>
            <code>REL</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2023-09-08</deposition>
            <header_release>2023-12-06</header_release>
            <map_release>2023-12-06</map_release>
            <update>2024-01-03</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Not funded</funding_body>
            </grant_reference>
        </grant_support>
        <title>De novo transcribing complex 10 (AdML10G), the early elongation complex with Pol II positioned 10nt downstream of TSS.</title>
        <authors_list>
            <author>Chen X</author>
            <author>Liu W</author>
            <author>Xu Y</author>
        </authors_list>
        <keywords>transcribing complex, de novo transcription initiation, early elongation complex (EEC), TRANSCRIPTION</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0002-4120-104X" order="1">Chen X</author>
                    <author ORCID="0000-0002-1242-2628" order="2">Liu W</author>
                    <author ORCID="0000-0002-4144-8931" order="3">Wang Q</author>
                    <author ORCID="0000-0001-5085-175X" order="4">Wang X</author>
                    <author ORCID="0000-0002-3512-237X" order="5">Ren Y</author>
                    <author ORCID="0000-0001-8958-4695" order="6">Qu X</author>
                    <author ORCID="0009-0002-2111-1087" order="7">Li W</author>
                    <author ORCID="0000-0002-1408-5178" order="8">Xu Y</author>
                    <title>Structural visualization of transcription initiation in action.</title>
                    <journal_abbreviation>Science</journal_abbreviation>
                    <country>US</country>
                    <volume>382</volume>
                    <first_page>eadi5120</first_page>
                    <last_page>eadi5120</last_page>
                    <year>2023</year>
                    <external_references type="PUBMED">38127763</external_references>
                    <external_references type="DOI">doi:10.1126/science.adi5120</external_references>
                    <external_references type="ISSN">1095-9203</external_references>
                    <external_references type="CSD">0038</external_references>
                    <external_references type="ASTM">SCIEAS</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-31111</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>TFIID-based holo PIC on SCP promoter</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-37412</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>De novo transcribing complex 9 (AdML9G), the initially transcribing complex with Pol II positioned 9nt downstream of TSS</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-37411</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>De novo transcribing complex 17 (TC17), the early elongation complex with Pol II positioned 17nt downstream of TSS.</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-37410</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>De novo transcribing complex 16 (TC16), the early elongation complex with Pol II positioned 16nt downstream of TSS.</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-37409</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>De novo transcribing complex 15 (TC15), the early elongation complex with Pol II positioned 15nt downstream of TSS.</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-37408</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>De novo transcribing complex 14 (TC14), the early elongation complex with Pol II positioned 14nt downstream of TSS.</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-37407</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>De novo transcribing complex 13 (TC13), the early elongation complex with Pol II positioned 13nt downstream of TSS.</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-37406</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>De novo transcribing complex 12 (TC12), the early elongation complex with Pol II positioned 12nt downstream of TSS.</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-37405</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>De novo transcribing complex 11 (TC11), the early elongation complex with Pol II positioned 11nt downstream of TSS.</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-37404</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>De novo transcribing complex 10 (TC10), the early elongation complex with Pol II positioned 10nt downstream of TSS.</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-37403</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>Structure of transcribing complex 9 (TC9), the initially transcribing complex with Pol II positioned 9nt downstream of TSS.</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-37402</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>Structure of transcribing complex 8 (TC8), the initially transcribing complex with Pol II positioned 8nt downstream of TSS.</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-37401</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>Structure of transcribing complex 7 (TC7), the initially transcribing complex with Pol II positioned 7nt downstream of TSS.</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-37400</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>Structure of transcribing complex 6 (TC6), the initially transcribing complex with Pol II positioned 6nt downstream of TSS.</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-37399</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>Structure of transcribing complex 5 (TC5), the initially transcribing complex with Pol II positioned 5nt downstream of TSS.</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-37398</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>Structure of transcribing complex 4 (TC4), the initially transcribing complex with Pol II positioned 4nt downstream of TSS.</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-37396</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>Structure of transcribing complex 3 (TC3), the initially transcribing complex with Pol II positioned 3nt downstream of TSS.</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-37395</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>Structure of transcribing complex 2 (TC2), the initially transcribing complex with Pol II positioned 2nt downstream of TSS.</details>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>De novo transcribing complex 10 (AdML10G), the early elongation complex with Pol II positioned 10nt downstream of TSS.</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>De novo transcribing complex 10 (AdML10G), the early elongation complex with Pol II positioned 10nt downstream of TSS.</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>3</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>4</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>5</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>6</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>7</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>8</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>9</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>10</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>11</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>12</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>13</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>14</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>15</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>16</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>17</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>18</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
            </complex_supramolecule>
            <complex_supramolecule supramolecule_id="2">
                <name>RNA POLYMERASE II</name>
                <parent>1</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>7</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>8</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>9</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>10</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>11</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>12</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>13</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>14</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>15</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>16</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>17</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>18</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="9823">Sus scrofa</organism>
                </natural_source>
            </complex_supramolecule>
            <complex_supramolecule supramolecule_id="3">
                <name>TFIIF</name>
                <parent>1</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>3</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
            </complex_supramolecule>
            <complex_supramolecule supramolecule_id="4">
                <name>DNA</name>
                <parent>1</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>4</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>5</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI" synthetically_produced="true">
                    <organism ncbi="32630">synthetic construct</organism>
                </natural_source>
            </complex_supramolecule>
            <complex_supramolecule supramolecule_id="5">
                <name>RNA</name>
                <parent>1</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>6</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI" synthetically_produced="true">
                    <organism ncbi="32630">synthetic construct</organism>
                </natural_source>
            </complex_supramolecule>
            <complex_supramolecule supramolecule_id="6">
                <name>Alpha-amanitin</name>
                <parent>1</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="67723">Amanita phalloides</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>7.9</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">1.5</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>GATAN K3 (6k 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="PDB ENTRY">
                    <pdb_model>
                        <pdb_id>5FLM</pdb_id>
                    </pdb_model>
                </startup_model>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">3.47</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <number_images_used>85241</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="131073">
        <file>emd_37413.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>320</col>
            <row>320</row>
            <sec>320</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>320</x>
            <y>320</y>
            <z>320</z>
        </spacing>
        <cell>
            <a units="Å">426.88</a>
            <b units="Å">426.88</b>
            <c units="Å">426.88</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>-1.8023806</minimum>
            <maximum>3.7154722</maximum>
            <average>0.004152581</average>
            <std>0.064929344</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.334</x>
            <y units="Å">1.334</y>
            <z units="Å">1.334</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.732</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-37413::::</label>
    </map>
    <interpretation>
        <additional_map_list>
            <additional_map format="CCP4" size_kbytes="131073">
                <file>emd_37413_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>320</col>
                    <row>320</row>
                    <sec>320</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>320</x>
                    <y>320</y>
                    <z>320</z>
                </spacing>
                <cell>
                    <a units="Å">426.88</a>
                    <b units="Å">426.88</b>
                    <c units="Å">426.88</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>-0.064512715</minimum>
                    <maximum>0.26786497</maximum>
                    <average>0.002292062</average>
                    <std>0.026425274</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.334</x>
                    <y units="Å">1.334</y>
                    <z units="Å">1.334</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-37413::::</label>
                <annotation_details>Overall map of AdML10G</annotation_details>
            </additional_map>
        </additional_map_list>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="131073">
                <file>emd_37413_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>320</col>
                    <row>320</row>
                    <sec>320</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>320</x>
                    <y>320</y>
                    <z>320</z>
                </spacing>
                <cell>
                    <a units="Å">426.88</a>
                    <b units="Å">426.88</b>
                    <c units="Å">426.88</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>-2.359441</minimum>
                    <maximum>2.6448503</maximum>
                    <average>0.003514607</average>
                    <std>0.18705782</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.334</x>
                    <y units="Å">1.334</y>
                    <z units="Å">1.334</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-37413::::</label>
            </half_map>
            <half_map format="CCP4" size_kbytes="131073">
                <file>emd_37413_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>320</col>
                    <row>320</row>
                    <sec>320</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>320</x>
                    <y>320</y>
                    <z>320</z>
                </spacing>
                <cell>
                    <a units="Å">426.88</a>
                    <b units="Å">426.88</b>
                    <c units="Å">426.88</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>-2.221303</minimum>
                    <maximum>2.9670935</maximum>
                    <average>0.0035159155</average>
                    <std>0.18692155</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.334</x>
                    <y units="Å">1.334</y>
                    <z units="Å">1.334</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-37413::::</label>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
