<?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_3/emdb.xsd" version="3.0.9.3" emdb_id="EMD-28816">
    <admin>
        <current_status>
            <date>2024-11-20</date>
            <code>OBS</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>2022-11-23</header_release>
            <map_release>2022-11-23</map_release>
            <obsolete>2024-11-20</obsolete>
            <update>2024-11-20</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Cancer Institute (NIH/NCI)</funding_body>
                <code>R01CA193578</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Cancer Institute (NIH/NCI)</funding_body>
                <code>R01CA227261</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Cancer Institute (NIH/NCI)</funding_body>
                <code>R01CA219700</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Wild type P53 dimer structure from human cancer cells</title>
        <authors_list>
            <author>Solares M</author>
            <author>Kelly DF</author>
        </authors_list>
        <keywords>cancer, tumor suppressor, cell cycle, apoptosis, DNA repair, ANTITUMOR PROTEIN</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Solares MJ</author>
                    <author order="2">Jonaid GM</author>
                    <author order="3">Luqiu WY</author>
                    <author order="4">Berry S</author>
                    <author order="5">Khadela J</author>
                    <author order="6">Liang Y</author>
                    <author order="7">Evans MC</author>
                    <author order="8">Pridham KJ</author>
                    <author order="9">Dearnaley WJ</author>
                    <author order="10">Sheng Z</author>
                    <author ORCID="0000-0002-7341-7435" order="11">Kelly DF</author>
                    <title>RETRACTION: High-Resolution Imaging of Human Cancer Proteins Using Microprocessor Materials</title>
                    <journal_abbreviation>Chembiochem</journal_abbreviation>
                    <country>GE</country>
                    <year>2024</year>
                    <external_references type="PUBMED">39497285</external_references>
                    <external_references type="DOI">doi:10.1002/cbic.202400798</external_references>
                    <external_references type="ISSN">1439-7633</external_references>
                </journal_citation>
            </primary_citation>
            <secondary_citation>
                <journal_citation published="true">
                    <author order="12">Solares MJ</author>
                    <author order="13">Jonaid GM</author>
                    <author order="14">Luqiu WY</author>
                    <author order="15">Berry S</author>
                    <author order="16">Khadela J</author>
                    <author order="17">Liang Y</author>
                    <author order="18">Evans MC</author>
                    <author order="19">Pridham KJ</author>
                    <author order="20">Dearnaley WJ</author>
                    <author order="21">Sheng Z</author>
                    <author ORCID="0000-0002-7341-7435" order="22">Kelly DF</author>
                    <title>High-Resolution Imaging of Human Cancer Proteins Using Microprocessor Materials.</title>
                    <journal_abbreviation>Chembiochem</journal_abbreviation>
                    <country>GE</country>
                    <volume>23</volume>
                    <first_page>e202200310</first_page>
                    <last_page>e202200310</last_page>
                    <year>2022</year>
                    <external_references type="PUBMED">35789183</external_references>
                    <external_references type="DOI">doi:10.1002/cbic.202200310</external_references>
                    <external_references type="ISSN">1439-7633</external_references>
                </journal_citation>
            </secondary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>8f2h</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>P53 dimer isolated from U87-MG cells</name>
        <supramolecule_list>
            <cell_supramolecule supramolecule_id="1">
                <name>P53 dimer isolated from U87-MG cells</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <details>Native protein, wild-type with no tags</details>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <organ>Brain</organ>
                    <tissue>Brain tumor</tissue>
                </natural_source>
            </cell_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Cellular tumor antigen p53</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <organ>brain tumor</organ>
                    <tissue>brain</tissue>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.043711176</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAP
TPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAM
AIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS
SCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKK
KPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD</string>
                    <external_references type="UNIPROTKB">P04637</external_references>
                </sequence>
            </protein_or_peptide>
        </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">0.2</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>20 mM HEPES (pH 7.5), 140 mM NaCl, 2 mM MgCl2, 2 mM CaCl2, 5 mM imidazole</details>
                    </buffer>
                    <grid>
                        <model>Homemade</model>
                        <material>SILICON NITRIDE</material>
                        <details>Silicon nitride chips coated with Ni-NTA layers prior to sample application</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <chamber_temperature units="K">298</chamber_temperature>
                        <instrument>FEI VITROBOT MARK III</instrument>
                        <details>The microchip samples were  loaded into a FEI Mark III Vitrobot and flash-frozen into liquid ethane.. </details>
                    </vitrification>
                    <details>Sample was placed on Silicon nitride chips coated with Ni-NTA layers</details>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>TFS TALOS F200C</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">100.0</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">5.0</nominal_defocus_max>
                    <nominal_magnification>142000.0</nominal_magnification>
                    <specimen_holder_model>GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <basic/>
                    </alignment_procedure>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI CETA (4k x 4k)</film_or_detector_model>
                            <digitization_details/>
                            <number_grids_imaged>10</number_grids_imaged>
                            <number_real_images>300</number_real_images>
                            <average_exposure_time units="s">1.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">5.0</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>8000</number_selected>
                </particle_selection>
                <startup_model type_of_model="NONE"/>
                <final_reconstruction>
                    <number_classes_used>1</number_classes_used>
                    <applied_symmetry>
                        <point_group>C2</point_group>
                    </applied_symmetry>
                    <algorithm>BACK PROJECTION</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">4.2</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                    <number_images_used>8000</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>ANGULAR RECONSTITUTION</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>ANGULAR RECONSTITUTION</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <number_classes>1</number_classes>
                    <average_number_members_per_class>8000.0</average_number_members_per_class>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="2825">
        <file>emd_28816.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>91</col>
            <row>97</row>
            <sec>80</sec>
        </dimensions>
        <origin>
            <col>-45</col>
            <row>-48</row>
            <sec>-39</sec>
        </origin>
        <spacing>
            <x>91</x>
            <y>97</y>
            <z>80</z>
        </spacing>
        <cell>
            <a units="Å">100.1</a>
            <b units="Å">106.700005</b>
            <c units="Å">88.0</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>-4.2792163</minimum>
            <maximum>8.506843</maximum>
            <average>0.000000000015819</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.1</x>
            <y units="Å">1.1</y>
            <z units="Å">1.1</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.2</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-28816::::</label>
        <annotation_details>P53 dimer structure</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
                <refinement_space>REAL</refinement_space>
                <overall_bvalue>50.0</overall_bvalue>
            </modelling>
        </modelling_list>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="2566">
                <file>emd_28816_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>87</col>
                    <row>97</row>
                    <sec>76</sec>
                </dimensions>
                <origin>
                    <col>-45</col>
                    <row>-48</row>
                    <sec>-39</sec>
                </origin>
                <spacing>
                    <x>87</x>
                    <y>97</y>
                    <z>76</z>
                </spacing>
                <cell>
                    <a units="Å">95.700005</a>
                    <b units="Å">106.700005</b>
                    <c units="Å">83.6</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>-8.706413</minimum>
                    <maximum>10.457101</maximum>
                    <average>-0.000000000013625</average>
                    <std>1.0</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.1</x>
                    <y units="Å">1.1</y>
                    <z units="Å">1.1</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-28816::::</label>
                <annotation_details>Half Map 2</annotation_details>
            </half_map>
            <half_map format="CCP4" size_kbytes="2566">
                <file>emd_28816_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>87</col>
                    <row>97</row>
                    <sec>76</sec>
                </dimensions>
                <origin>
                    <col>-45</col>
                    <row>-48</row>
                    <sec>-39</sec>
                </origin>
                <spacing>
                    <x>87</x>
                    <y>97</y>
                    <z>76</z>
                </spacing>
                <cell>
                    <a units="Å">95.700005</a>
                    <b units="Å">106.700005</b>
                    <c units="Å">83.6</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>-6.3088307</minimum>
                    <maximum>9.377618999999999</maximum>
                    <average>0.000000000051426</average>
                    <std>1.0</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.1</x>
                    <y units="Å">1.1</y>
                    <z units="Å">1.1</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-28816::::</label>
                <annotation_details>Half Map 1</annotation_details>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
