<?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-24530">
    <admin>
        <current_status>
            <date>2024-06-05</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2021-07-23</deposition>
            <header_release>2021-09-22</header_release>
            <map_release>2021-09-22</map_release>
            <update>2024-06-05</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Not funded</funding_body>
            </grant_reference>
        </grant_support>
        <title>Cryo-EM structure of human p97-D592N mutant bound to ATPgS.</title>
        <authors_list>
            <author>Caffrey B</author>
            <author>Zhu X</author>
        </authors_list>
        <keywords>p97, VCP, TERA, Inhibitor, CB-5083, HYDROLASE</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Caffrey B</author>
                    <author order="2">Zhu X</author>
                    <author order="3">Berezuk A</author>
                    <author order="4">Tuttle K</author>
                    <author order="5">Chittori S</author>
                    <author order="6">Subramaniam S</author>
                    <title>AAA+ ATPase p97/VCP mutants and inhibitor binding disrupt inter-domain coupling and subsequent allosteric activation.</title>
                    <journal_abbreviation>J.Biol.Chem.</journal_abbreviation>
                    <country>US</country>
                    <volume>297</volume>
                    <first_page>101187</first_page>
                    <last_page>101187</last_page>
                    <year>2021</year>
                    <external_references type="PUBMED">34520757</external_references>
                    <external_references type="DOI">doi:10.1016/j.jbc.2021.101187</external_references>
                    <external_references type="ISSN">1083-351X</external_references>
                    <external_references type="CSD">0071</external_references>
                    <external_references type="ASTM">JBCHA3</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>7rlh</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Full-length Hexameric p97-D592N mutant.</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Full-length Hexameric p97-D592N mutant.</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.540</theoretical>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Transitional endoplasmic reticulum ATPase</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.08943583599999999</theoretical>
                </molecular_weight>
                <number_of_copies>6</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="469008">Escherichia coli BL21(DE3)</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDE
KIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRA
VEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRG
ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEV
ERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVA
NETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIG
GLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVR
EIFDKARQAAPCVLFFDELDSIAKARGGNIGNGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLD
QLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAM
EVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPSGNQGGAGPSQGSGGGTGGSVYTEDN
DDDLYG</string>
                    <external_references type="UNIPROTKB">P55072</external_references>
                </sequence>
                <ec_number>3.6.4.6</ec_number>
            </protein_or_peptide>
            <ligand macromolecule_id="2">
                <name>PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER</name>
                <molecular_weight>
                    <theoretical units="MDa">0.0005232469999999999</theoretical>
                </molecular_weight>
                <number_of_copies>12</number_of_copies>
                <formula>AGS</formula>
            </ligand>
            <ligand macromolecule_id="3">
                <name>MAGNESIUM ION</name>
                <molecular_weight>
                    <theoretical units="MDa">2.4305e-05</theoretical>
                </molecular_weight>
                <number_of_copies>12</number_of_copies>
                <formula>MG</formula>
            </ligand>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>singleParticle</method>
            <aggregation_state>twoDArray</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <concentration units="mg/mL">2</concentration>
                    <buffer>
                        <ph>8.0</ph>
                        <component>
                            <concentration units="mM">150.0</concentration>
                            <formula>NaCl</formula>
                            <name>Sodium Chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">50.0</concentration>
                            <formula>Tris-HCl</formula>
                            <name>Tris Hydrochloride</name>
                        </component>
                        <component>
                            <concentration units="mM">5.0</concentration>
                            <formula>MgCl2</formula>
                            <name>Magnesium Chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">1.0</concentration>
                            <formula>C9H15O6P</formula>
                            <name>TCEP</name>
                        </component>
                        <component>
                            <concentration units="mM">1.0</concentration>
                            <formula>C10H12N5O12P3S</formula>
                            <name>ATPgS</name>
                        </component>
                        <details>Protein Storage Buffer with ATPgS.</details>
                    </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>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI FALCON IV (4k x 4k)</film_or_detector_model>
                            <number_real_images>4464</number_real_images>
                            <average_electron_dose_per_image units="e/Å^2">40.0</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>299730</number_selected>
                </particle_selection>
                <startup_model type_of_model="INSILICO MODEL"/>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">3.0</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <number_images_used>175007</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_24530.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">320.0</a>
            <b units="Å">320.0</b>
            <c units="Å">320.0</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>-0.42420402</minimum>
            <maximum>2.22638</maximum>
            <average>0.0005278461</average>
            <std>0.05442903</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>0.25</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-24530::::</label>
        <annotation_details>Cryo-EM structure of human p97-D592N bound to ATPgS.</annotation_details>
    </map>
</emd>
