<?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_2/emdb.xsd" version="3.0.9.2" emdb_id="EMD-28818">
    <admin>
        <current_status>
            <date>2024-04-24</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2022-11-08</deposition>
            <header_release>2023-04-05</header_release>
            <map_release>2023-04-05</map_release>
            <update>2024-04-24</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Canada Research Chairs</funding_body>
                <code>Electron Cryomicroscopy</code>
                <country>Canada</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Canadian Institutes of Health Research (CIHR)</funding_body>
                <code>PJT162186</code>
                <country>Canada</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Canada Foundation for Innovation</funding_body>
                <country>Canada</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Cancer Institute (NIH/NCI)</funding_body>
                <code>R01 CA216919</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)</funding_body>
                <code>UL1TR002529</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Structure of yeast F1-ATPase determined with 100 micromolar cruentaren A</title>
        <authors_list>
            <author>Guo H</author>
            <author>Rubinstein JL</author>
        </authors_list>
        <keywords>F1-ATPase, ATP Synthase, cruentaren A, drug development, HYDROLASE</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Dou X</author>
                    <author order="2">Guo H</author>
                    <author order="3">D'Amico T</author>
                    <author order="4">Abdallah L</author>
                    <author order="5">Subramanian C</author>
                    <author order="6">Patel BA</author>
                    <author order="7">Cohen M</author>
                    <author order="8">Rubinstein JL</author>
                    <author ORCID="0000-0002-6200-3480" order="9">Blagg BSJ</author>
                    <title>CryoEM Structure with ATP Synthase Enables Late-Stage Diversification of Cruentaren A.</title>
                    <journal_abbreviation>Chemistry</journal_abbreviation>
                    <country>GE</country>
                    <volume>29</volume>
                    <first_page>e202300262</first_page>
                    <last_page>e202300262</last_page>
                    <year>2023</year>
                    <external_references type="PUBMED">36867738</external_references>
                    <external_references type="DOI">doi:10.1002/chem.202300262</external_references>
                    <external_references type="ISSN">0947-6539</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>8f2k</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Yeast F1-ATPase with 100 micromolar cruentaren A</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Yeast F1-ATPase with 100 micromolar cruentaren A</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_list>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                    <strain>USY006</strain>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.4</theoretical>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>ATP synthase subunit alpha</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.05237653899999999</theoretical>
                </molecular_weight>
                <number_of_copies>3</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>NLNETGRVLAVGDGIARVFGLNNIQAEELVEFSSGVKGMALNLEPGQVGIVLFGSDRLVKEGELVKRTGNIVDVPVGPGL
LGRVVDALGNPIDGKGPIDAAGRSRAQVKAPGILPRRSVHEPVQTGLKAVDALVPIGRGQRELIIGDRQTGKTAVALDTI
LNQKRWNNGSDESKKLYCVYVAVGQKRSTVAQLVQTLEQHDAMKYSIIVAATASEAAPLQYLAPFTAASIGEWFRDNGKH
ALIVYDDLSKQAVAYRQLSLLLRRPPGREAYPGDVFYLHSRLLERAAKLSEKEGSGSLTALPVIETQGGDVSAYIPTNVI
SITDGQIFLEAELFYKGIRPAINVGLSVSRVGSAAQVKALKQVAGSLKLFLAQYREVAAFAQFGSDLDASTKQTLVRGER
LTQLLKQNQYSPLATEEQVPLIYAGVNGHLDGIELSRIGEFESSFLSYLKSNHNELLTEIREKGELSKELLASLKSATES
FVATF</string>
                    <external_references type="UNIPROTKB">A0A6A5Q4L9</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>ATP synthase subunit beta</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.050379277</theoretical>
                </molecular_weight>
                <number_of_copies>3</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>PITGKVTAVIGAIVDVHFEQSELPAILNALEIKTPQGKLVLEVAQHLGENTVRTIAMDGTEGLVRGEKVLDTGGPISVPV
GRETLGRIINVIGEPIDERGPIKSKLRKPIHADPPSFAEQSTSAEILETGIKVVDLLAPYARGGKIGLFGGAGVGKTVFI
QELINNIAKAHGGFSVFTGVGERTREGNDLYREMKETGVINLEGESKVALVFGQMNEPPGARARVALTGLTIAEYFRDEE
GQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGLLQERITTTKKGSVTSVQAVYVPADDLTDPAPATTFA
HLDATTVLSRGISELGIYPAVDPLDSKSRLLDAAVVGQEHYDVASKVQETLQTYKSLQDIIAILGMDELSEQDKLTVERA
RKIQRFLSQPFAVAEVFTGIPGKLVRLKDTVASFKAVLEGKYDNIPEHAFYMVGGIEDVVAKAEKLAAE</string>
                    <external_references type="UNIPROTKB">A0A6A5PX46</external_references>
                </sequence>
                <ec_number>7.1.2.2</ec_number>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name>ATP synthase subunit gamma</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.030399875</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>ATLKEVEMRLKSIKNIEKITKTMKIVASTRLSKAEKAKISAKKMDEAEQLFYKNAETKNLDVEATETGAPKELIVAITSD
KGLCGSIHSQLAKAVRRHLNDQPNADIVTIGDKIKMQLLRTHPNNIKLSINGIGKDAPTFQESALIADKLLSVMKAGTYP
KISIFYNDPVSSLSFEPSEKPIFNAKTIEQSPSFGKFEIDTDANVPRDLFEYTLANQMLTAMAQGYAAEISARRNAMDNA
SKNAGDMINRYSILYNRTRQAVITNELVDIITGAS</string>
                    <external_references type="UNIPROTKB">A0A6A5Q493</external_references>
                </sequence>
            </protein_or_peptide>
            <ligand macromolecule_id="4">
                <name>ADENOSINE-5'-TRIPHOSPHATE</name>
                <molecular_weight>
                    <theoretical units="MDa">0.000507181</theoretical>
                </molecular_weight>
                <number_of_copies>5</number_of_copies>
                <formula>ATP</formula>
            </ligand>
            <ligand macromolecule_id="5">
                <name>MAGNESIUM ION</name>
                <molecular_weight>
                    <theoretical units="MDa">2.4305e-05</theoretical>
                </molecular_weight>
                <number_of_copies>5</number_of_copies>
                <formula>MG</formula>
            </ligand>
            <ligand macromolecule_id="6">
                <name>Cruentaren A</name>
                <molecular_weight>
                    <theoretical units="MDa">0.0005897599999999999</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <formula>XBC</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">15</concentration>
                    <buffer>
                        <ph>7.4</ph>
                    </buffer>
                    <grid>
                        <model>Homemade</model>
                        <material>COPPER/RHODIUM</material>
                        <mesh>300</mesh>
                        <support_film film_type_id="1">
                            <film_material>GOLD</film_material>
                            <film_topology>HOLEY</film_topology>
                            <film_thickness>35.0</film_thickness>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <time units="s">120</time>
                            <atmosphere>OTHER</atmosphere>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE-PROPANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">277</chamber_temperature>
                        <instrument>LEICA EM GP</instrument>
                    </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>
                    <c2_aperture_diameter units="µm">50.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">2.0</nominal_defocus_max>
                    <nominal_magnification>75000.0</nominal_magnification>
                    <calibrated_magnification>133815.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <zemlin_tableau/>
                    </alignment_procedure>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI FALCON IV (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">4096</width>
                                    <height units="pixel">4096</height>
                                </dimensions>
                            </digitization_details>
                            <number_real_images>5814</number_real_images>
                            <average_exposure_time units="s">8.4</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">42.0</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>1352159</number_selected>
                </particle_selection>
                <startup_model type_of_model="OTHER"/>
                <final_reconstruction>
                    <number_classes_used>3</number_classes_used>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <algorithm>BACK PROJECTION</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">2.9</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>3.1.0</version>
                        </software>
                    </software_list>
                    <number_images_used>701444</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>3.1.0</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>3.1.0</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <number_classes>3</number_classes>
                    <average_number_members_per_class>233814.0</average_number_members_per_class>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>3.1.0</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="131073">
        <file>emd_28818.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">334.79037</a>
            <b units="Å">334.79037</b>
            <c units="Å">334.79037</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>-7.164443</minimum>
            <maximum>10.720364999999999</maximum>
            <average>0.00116477</average>
            <std>0.18358803</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.04622</x>
            <y units="Å">1.04622</y>
            <z units="Å">1.04622</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.1</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-28818::::</label>
        <annotation_details>Sharpened map.</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>2HLD</access_code>
                    <chain>
                        <source_name>PDB</source_name>
                        <initial_model_type>experimental model</initial_model_type>
                    </chain>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <refinement_space>RECIPROCAL</refinement_space>
            </modelling>
        </modelling_list>
        <segmentation_list>
            <segmentation>
                <file>emd_28818_msk_1.map</file>
            </segmentation>
        </segmentation_list>
        <additional_map_list>
            <additional_map format="CCP4" size_kbytes="131073">
                <file>emd_28818_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">334.79037</a>
                    <b units="Å">334.79037</b>
                    <c units="Å">334.79037</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>-0.5853757</minimum>
                    <maximum>2.5342975</maximum>
                    <average>0.0011647699</average>
                    <std>0.08822183</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.04622</x>
                    <y units="Å">1.04622</y>
                    <z units="Å">1.04622</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-28818::::</label>
                <annotation_details>Unsharpened map.</annotation_details>
            </additional_map>
        </additional_map_list>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="131073">
                <file>emd_28818_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">334.79037</a>
                    <b units="Å">334.79037</b>
                    <c units="Å">334.79037</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>-0.87252474</minimum>
                    <maximum>2.7469013</maximum>
                    <average>0.0032598404</average>
                    <std>0.10296936</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.04622</x>
                    <y units="Å">1.04622</y>
                    <z units="Å">1.04622</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-28818::::</label>
                <annotation_details>Half map 2.</annotation_details>
            </half_map>
            <half_map format="CCP4" size_kbytes="131073">
                <file>emd_28818_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">334.79037</a>
                    <b units="Å">334.79037</b>
                    <c units="Å">334.79037</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>-1.0447924</minimum>
                    <maximum>2.7747962</maximum>
                    <average>0.0032354104</average>
                    <std>0.102942646</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.04622</x>
                    <y units="Å">1.04622</y>
                    <z units="Å">1.04622</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-28818::::</label>
                <annotation_details>Half map 1.</annotation_details>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
