<?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-65128">
    <admin>
        <current_status>
            <date>2025-11-12</date>
            <code>REL</code>
            <processing_site>PDBc</processing_site>
        </current_status>
        <revision_history>
            <revision version="1.0" date="2025-11-05">
                <change_list>
                    <model>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </model>
                </change_list>
            </revision>
            <revision version="1.1" date="2025-11-12">
                <change_list>
                    <model>
                        <revision_group>STRUCTURE_SUMMARY</revision_group>
                        <categories>
                            <category>citation</category>
                            <category>em_admin</category>
                            <category>struct</category>
                        </categories>
                        <items>
                            <item>_citation.journal_volume</item>
                            <item>_em_admin.last_update</item>
                            <item>_em_admin.title</item>
                            <item>_struct.title</item>
                        </items>
                    </model>
                </change_list>
            </revision>
        </revision_history>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBc</last_processing>
        </sites>
        <key_dates>
            <deposition>2025-06-22</deposition>
            <header_release>2025-11-05</header_release>
            <map_release>2025-11-05</map_release>
            <update>2025-11-12</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Natural Science Foundation of China (NSFC)</funding_body>
                <code>32000852</code>
                <country>China</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Natural Science Foundation of China (NSFC)</funding_body>
                <code>31925024</code>
                <country>China</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Chinese Academy of Sciences</funding_body>
                <code>YSBR-015</code>
                <country>China</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Chinese Academy of Sciences</funding_body>
                <code>XDB37020101</code>
                <country>China</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Chinese Academy of Sciences</funding_body>
                <code>ZDBS-LY-SM003</code>
                <country>China</country>
            </grant_reference>
        </grant_support>
        <title>Structure of the plant diacylglycerol O-acyltransferase 1 in complex with oleoyl-CoA</title>
        <authors_list>
            <author>Liu XY</author>
            <author>Li JJ</author>
            <author>Song DF</author>
            <author>Liu ZF</author>
        </authors_list>
        <keywords>TAG synthysis, activity regulation, FFA, intramembrane enzyme, MEMBRANE PROTEIN</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0002-3144-2499" order="1">Liu X</author>
                    <author ORCID="0009-0000-2326-4242" order="2">Li J</author>
                    <author ORCID="0000-0001-6785-173X" order="3">Song D</author>
                    <author ORCID="0000-0001-5502-9474" order="4">Liu Z</author>
                    <title>Structural mechanisms underlying the free fatty acid-mediated regulation of DIACYLGLYCEROL O-ACYLTRANSFERASE 1 in Arabidopsis.</title>
                    <journal_abbreviation>Plant Cell</journal_abbreviation>
                    <country>US</country>
                    <volume>37</volume>
                    <year>2025</year>
                    <external_references type="PUBMED">41081525</external_references>
                    <external_references type="DOI">doi:10.1093/plcell/koaf239</external_references>
                    <external_references type="ISSN">1532-298X</external_references>
                    <external_references type="CSD">2109</external_references>
                    <external_references type="ASTM">PLCEEW</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>9vk1</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
        <other_db_list>
            <db_reference>
                <db_name>EMDB</db_name>
                <accession_id>EMD-65128</accession_id>
                <content_type>associated EM volume</content_type>
                <details>Structure of plant diacylglycerol O-acyltransferase 1</details>
            </db_reference>
        </other_db_list>
    </crossreferences>
    <sample>
        <name>Dimer of plant diacylglycerol O-acyltransferase 1 with Oleoyl-CoA</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Dimer of plant diacylglycerol O-acyltransferase 1 with Oleoyl-CoA</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="3702">Arabidopsis thaliana</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.12</theoretical>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Diacylglycerol O-acyltransferase 1</name>
                <natural_source database="NCBI">
                    <organism ncbi="3702">Arabidopsis thaliana</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.060029699</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="4922">Komagataella pastoris</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MAILDSAGVTTVTENGGGEFVDLDRLRRRKSRSDSSNGLLLSGSDNNSPSDDVGAPADVRDRIDSVVNDDAQGTANLAGD
NNGGGDNNGGGRGGGEGRGNADATFTYRPSVPAHRRARESPLSSDAIFKQSHAGLFNLCVVVLIAVNSRLIIENLMKYGW
LIRTDFWFSSRSLRDWPLFMCCISLSIFPLAAFTVEKLVLQKYISEPVVIFLHIIITMTEVLYPVYVTLRCDSAFLSGVT
LMLLTCIVWLKLVSYAHTSYDIRSLANAADKANPEVSYYVSLKSLAYFMVAPTLCYQPSYPRSACIRKGWVARQFAKLVI
FTGFMGFIIEQYINPIVRNSKHPLKGDLLYAIERVLKLSVPNLYVWLCMFYCFFHLWLNILAELLCFGDREFYKDWWNAK
SVGDYWRMWNMPVHKWMVRHIYFPCLRSKIPKTLAIIIAFLVSAVFHELCIAVPCRLFKLWAFLGIMFQVPLVFITNYLQ
ERFGSTVGNMIFWFIFCIFGQPMCVLLYYHDLMNRKGSMSGPHHHHHH</string>
                    <external_references type="UNIPROTKB">Q9SLD2</external_references>
                </sequence>
                <ec_number>2.3.1.20</ec_number>
            </protein_or_peptide>
            <ligand macromolecule_id="2">
                <name>S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name)</name>
                <molecular_weight>
                    <theoretical units="MDa">0.00103198</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <formula>3VV</formula>
            </ligand>
        </macromolecule_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">0.48</concentration>
                    <buffer>
                        <ph>7.5</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">277.15</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>
                    <nominal_defocus_min units="µm">1.2</nominal_defocus_min>
                    <nominal_defocus_max units="µm">1.7</nominal_defocus_max>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (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>
                <particle_selection>
                    <number_selected>3313037</number_selected>
                </particle_selection>
                <ctf_correction>
                    <type>PHASE FLIPPING AND AMPLITUDE CORRECTION</type>
                </ctf_correction>
                <startup_model type_of_model="OTHER"/>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">3.54</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>V3.1</version>
                        </software>
                    </software_list>
                    <number_images_used>462401</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="67109">
        <file>emd_65128.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>256</col>
            <row>256</row>
            <sec>256</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>256</x>
            <y>256</y>
            <z>256</z>
        </spacing>
        <cell>
            <a units="Å">256.0</a>
            <b units="Å">256.0</b>
            <c units="Å">256.0</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>-2.128519</minimum>
            <maximum>2.9119916</maximum>
            <average>-0.00004981628</average>
            <std>0.059145994</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.0</x>
            <y units="Å">1.0</y>
            <z units="Å">1.0</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.4</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-65128::::</label>
    </map>
    <interpretation>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="67109">
                <file>emd_65128_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>256</col>
                    <row>256</row>
                    <sec>256</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>256</x>
                    <y>256</y>
                    <z>256</z>
                </spacing>
                <cell>
                    <a units="Å">256.0</a>
                    <b units="Å">256.0</b>
                    <c units="Å">256.0</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>-0.39985278</minimum>
                    <maximum>0.965915</maximum>
                    <average>0.0016544478</average>
                    <std>0.038097166</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.0</x>
                    <y units="Å">1.0</y>
                    <z units="Å">1.0</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-65128::::</label>
            </half_map>
            <half_map format="CCP4" size_kbytes="67109">
                <file>emd_65128_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>256</col>
                    <row>256</row>
                    <sec>256</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>256</x>
                    <y>256</y>
                    <z>256</z>
                </spacing>
                <cell>
                    <a units="Å">256.0</a>
                    <b units="Å">256.0</b>
                    <c units="Å">256.0</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>-0.35783082</minimum>
                    <maximum>0.9093526</maximum>
                    <average>0.0016541841</average>
                    <std>0.038060926</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.0</x>
                    <y units="Å">1.0</y>
                    <z units="Å">1.0</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-65128::::</label>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
