<?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-41056">
    <admin>
        <current_status>
            <date>2026-05-13</date>
            <code>OBS</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <revision_history>
            <revision version="1.0" date="2023-06-21">
                <change_list>
                    <metadata>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </metadata>
                    <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>
                    <primary_map>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </primary_map>
                </change_list>
            </revision>
            <revision version="1.1" date="2026-05-13">
                <change_list>
                    <metadata>
                        <revision_type>OBSOLETE</revision_type>
                        <provider>REPOSITORY</provider>
                        <revision_group>EXPERIMENTAL_SUMMARY</revision_group>
                        <categories>
                            <category>citation</category>
                            <category>citation_author</category>
                            <category>em_admin</category>
                            <category>em_supersede</category>
                        </categories>
                        <items>
                            <item>_em_admin.current_status</item>
                            <item>_em_admin.last_update</item>
                        </items>
                    </metadata>
                </change_list>
            </revision>
        </revision_history>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2023-06-13</deposition>
            <header_release>2023-06-21</header_release>
            <map_release>2023-06-21</map_release>
            <obsolete>2026-05-13</obsolete>
            <update>2026-05-13</update>
        </key_dates>
        <superseded_by_list>
            <entry>
                <date>2026-05-13</date>
                <entry>EMD-76932</entry>
            </entry>
        </superseded_by_list>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>GM111730</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Michael J. Fox Foundation</funding_body>
                <code>ASAP-000350</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Local refinement map (1/2) of the human PI3KC3-C1 complex (EMD-40669)</title>
        <authors_list>
            <author>Chen M</author>
            <author>Hurley JH</author>
        </authors_list>
        <keywords>Autophagy, Lipid kinase, Complex, IMMUNE SYSTEM</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0002-7668-3974" order="1">Chen M</author>
                    <author ORCID="0000-0001-9698-0020" order="2">Nguyen TN</author>
                    <author ORCID="0000-0002-4822-4316" order="3">Ren X</author>
                    <author ORCID="0000-0002-2550-0605" order="4">Khuu G</author>
                    <author ORCID="0000-0001-6415-9107" order="5">Cook ASI</author>
                    <author ORCID="0000-0003-1458-5321" order="6">Zhao Y</author>
                    <author ORCID="0000-0003-4792-174X" order="7">Yildiz A</author>
                    <author ORCID="0000-0003-2150-5545" order="8">Lazarou M</author>
                    <author ORCID="0000-0001-5054-5445" order="9">Hurley JH</author>
                    <title>Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex.</title>
                    <journal_abbreviation>Nat.Struct.Mol.Biol.</journal_abbreviation>
                    <country>US</country>
                    <year>2025</year>
                    <external_references type="PUBMED">40442316</external_references>
                    <external_references type="DOI">doi:10.1038/s41594-025-01557-x</external_references>
                    <external_references type="ISSN">1545-9985</external_references>
                </journal_citation>
            </primary_citation>
            <secondary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0002-7668-3974" order="10">Chen M</author>
                    <author ORCID="0000-0002-4822-4316" order="11">Ren X</author>
                    <author ORCID="0000-0001-6415-9107" order="12">Cook A</author>
                    <author ORCID="0000-0001-5054-5445" order="13">Hurley JH</author>
                    <title>Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex</title>
                    <journal_abbreviation>bioRxiv</journal_abbreviation>
                    <country>US</country>
                    <year>2023</year>
                    <external_references type="DOI">doi:10.1101/2023.06.01.543278</external_references>
                    <external_references type="ISSN">2692-8205</external_references>
                </journal_citation>
            </secondary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-40669</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>composite map</details>
            </emdb_reference>
        </emdb_list>
        <other_db_list>
            <db_reference>
                <db_name>EMDB</db_name>
                <accession_id>EMD-40669</accession_id>
                <content_type>other EM volume</content_type>
                <details>composite map</details>
            </db_reference>
            <db_reference>
                <db_name>EMDB</db_name>
                <accession_id>EMD-41056</accession_id>
                <content_type>associated EM volume</content_type>
            </db_reference>
        </other_db_list>
    </crossreferences>
    <sample>
        <name>Human autophagy initiation PI3KC3-C1 complex</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Human autophagy initiation PI3KC3-C1 complex</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_list>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.362</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">0.25</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <component>
                            <concentration units="mM">25.0</concentration>
                            <formula>C8H18N2O4S</formula>
                            <name>HEPES</name>
                        </component>
                        <component>
                            <concentration units="mM">300.0</concentration>
                            <formula>NaCl</formula>
                            <name>sodium chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">1.0</concentration>
                            <formula>MgCl2</formula>
                            <name>magnesium chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">25.0</concentration>
                            <formula>C9H15O6P</formula>
                            <name>TCEP</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R1.2/1.3</model>
                        <material>COPPER</material>
                        <mesh>300</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <details>25 mA</details>
                    </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>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TALOS 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">50.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">0.8</nominal_defocus_min>
                    <nominal_defocus_max units="µm">2.0</nominal_defocus_max>
                    <nominal_magnification>36000.0</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>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>2243</number_real_images>
                            <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>
                <particle_selection>
                    <number_selected>1229932</number_selected>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>3.3.1</version>
                        </software>
                    </software_list>
                    <type>PHASE FLIPPING AND AMPLITUDE CORRECTION</type>
                </ctf_correction>
                <startup_model type_of_model="INSILICO MODEL"/>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">3.28</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>3.3.1</version>
                        </software>
                    </software_list>
                    <number_images_used>226147</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>3.3.1</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>3.3.1</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <number_classes>4</number_classes>
                    <average_number_members_per_class>266147.0</average_number_members_per_class>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>3.3.1</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="186625">
        <file>emd_41056.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">401.4</a>
            <b units="Å">401.4</b>
            <c units="Å">401.4</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>-1.1963131</minimum>
            <maximum>2.337667</maximum>
            <average>-0.0002075661</average>
            <std>0.023898743</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.115</x>
            <y units="Å">1.115</y>
            <z units="Å">1.115</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.4</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-41056::::</label>
        <annotation_details>Local refinement map (1/2) of the human PI3KC3-C1 complex (EMD-40669)</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <chain>
                        <source_name>AlphaFold</source_name>
                        <initial_model_type>in silico model</initial_model_type>
                    </chain>
                </initial_model>
                <refinement_protocol>AB INITIO MODEL</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="186625">
                <file>emd_41056_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>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">401.4</a>
                    <b units="Å">401.4</b>
                    <c units="Å">401.4</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>-0.60082257</minimum>
                    <maximum>1.2334691</maximum>
                    <average>0.0003064134</average>
                    <std>0.054164324</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.115</x>
                    <y units="Å">1.115</y>
                    <z units="Å">1.115</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-41056::::</label>
                <annotation_details>The according half map (1/2)</annotation_details>
            </half_map>
            <half_map format="CCP4" size_kbytes="186625">
                <file>emd_41056_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>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">401.4</a>
                    <b units="Å">401.4</b>
                    <c units="Å">401.4</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>-0.60563934</minimum>
                    <maximum>1.4333018</maximum>
                    <average>0.0003096288</average>
                    <std>0.054103687</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.115</x>
                    <y units="Å">1.115</y>
                    <z units="Å">1.115</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-41056::::</label>
                <annotation_details>The according half map (2/2)</annotation_details>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
