<?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_7/emdb.xsd" version="3.0.11.7" emdb_id="EMD-25139">
    <admin>
        <current_status>
            <date>2026-08-12</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <revision_history>
            <revision version="1.0" date="2022-03-16">
                <change_list>
                    <model>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </model>
                    <metadata>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </metadata>
                </change_list>
            </revision>
            <revision version="1.1" date="2026-08-12">
                <change_list>
                    <metadata>
                        <revision_group>EXPERIMENTAL_SUMMARY</revision_group>
                        <categories>
                            <category>em_admin</category>
                        </categories>
                        <items>
                            <item>_em_admin.last_update</item>
                        </items>
                    </metadata>
                </change_list>
            </revision>
            <revision version="1.2" date="2026-08-12">
                <change_list>
                    <model>
                        <revision_type>REMEDIATION</revision_type>
                        <provider>REPOSITORY</provider>
                        <description>Metalloprotein remediation</description>
                        <revision_group>STRUCTURE_SUMMARY</revision_group>
                        <categories>
                            <category>em_admin</category>
                            <category>pdbx_entry_details</category>
                            <category>pdbx_modification_feature</category>
                            <category>pdbx_nonpoly_atom_coordination</category>
                            <category>pdbx_nonpoly_atom_coordination_sphere</category>
                            <category>pdbx_nonpoly_atom_coordination_sphere_order</category>
                            <category>pdbx_struct_conn_angle</category>
                            <category>struct_conn</category>
                        </categories>
                        <items>
                            <item>_em_admin.last_update</item>
                            <item>_pdbx_entry_details.has_protein_modification</item>
                        </items>
                    </model>
                </change_list>
            </revision>
        </revision_history>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2021-10-12</deposition>
            <header_release>2022-03-16</header_release>
            <map_release>2022-03-16</map_release>
            <update>2026-08-12</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)</funding_body>
                <code>NS109307</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Cancer Institute (NIH/NCI)</funding_body>
                <code>P30 CA008748</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Structure of ATP7B in state 2</title>
        <authors_list>
            <author>Bitter RM</author>
            <author>Oh SC</author>
        </authors_list>
        <keywords>Copper transport, Wilson disease, METAL TRANSPORT, Translocase</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0001-9272-3609" order="1">Bitter RM</author>
                    <author ORCID="0000-0002-1685-5922" order="2">Oh S</author>
                    <author ORCID="0000-0002-5658-2068" order="3">Deng Z</author>
                    <author ORCID="0000-0002-7946-5155" order="4">Rahman S</author>
                    <author ORCID="0000-0003-0496-0669" order="5">Hite RK</author>
                    <author ORCID="0000-0002-5660-225X" order="6">Yuan P</author>
                    <title>Structure of the Wilson disease copper transporter ATP7B.</title>
                    <journal_abbreviation>Sci Adv</journal_abbreviation>
                    <country>US</country>
                    <volume>8</volume>
                    <first_page>eabl5508</first_page>
                    <last_page>eabl5508</last_page>
                    <year>2022</year>
                    <external_references type="PUBMED">35245129</external_references>
                    <external_references type="DOI">doi:10.1126/sciadv.abl5508</external_references>
                    <external_references type="ISSN">2375-2548</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>7si7</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-25139</accession_id>
                <content_type>associated EM volume</content_type>
                <details>Structure of ATP7B in state 2</details>
            </db_reference>
        </other_db_list>
    </crossreferences>
    <sample>
        <name>ATP7B</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>ATP7B</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="8364">Xenopus tropicalis</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>P-type Cu(+) transporter</name>
                <natural_source database="NCBI">
                    <organism ncbi="8364">Xenopus tropicalis</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.159678672</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="4922">Komagataella pastoris</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MFPKRILDEEEGVQLLSTENEKCSTKRRSSPQFCVNNTFSDSPVSVWKEAKKPSCAFDNRGYEGSPDDLCSLPDDVGSVV
VAIQGMTCQSCVQSIEGRISKVSGVVGINVCLEQNNAIVNYLQTEITPHKICEEIEDMGFDASLSEQSGMPSSVKSSYYG
DNVIKIRVEGMTCQSCVNTIEGKIGKIQGVQKIKVSLTGQEAVITYQSHIIQAEDLRKYIEDMGFEASIKNKPDPTKLGT
IDIERLQNSIAENHSGHTNSNTVTLGIDGMHCKSCVHNIEGYVSGLAGIQSIRVSLKNKNAVVCLSQGSTSLLSLKESIE
NLPPGKFKVTLPVGVEKGQSLARNSTHSSHRDQSMGGNIAIISIGGMTCQSCVSSIENMISQRKGVLHILVSLDEGNGNI
FYNPCETNAEELRAAIEDMGFHSTLVSDNSPSISCSEYNSKEEENKQTPPKATRQISGSRDYILDVLPKKSHPDFANEKY
DTAPEKCFLQITGMTCISCVSNIERNLKKKDGIVSVLVALMSGKAEVKFYPDRIEPLEIAQLVEDLGFGASVMEDYTASD
GNVELIITGMTCASCVHNIESRLMRTPGILQASVALATCKAQVKFDPEIVGPRDIIRIIEGIGFQASLAKRDPTAHKLDH
KEEIKQWRNSFLFSLLFGIPVIILMIYMLAANKDHHNTMVLDRNIVPGLSIINLVFFILCTFVQTLGGRYFYVQAYKSLK
HKATNMDVLIVLATTIAYIYSVVILTVAMVEKADKSPETFFDTPPMLFMFIALGRWLEHIAKSKTSEALAKLISLQATEA
AVVTFGANQIILREEQVAVELVQRGDIVKVVPGGKFPVDGKVIEGTSMADESLITGEPMPVRKKPGSMVIAGSINAHGTV
LVEATHVGSETTLAQIVKLVEEAQMSKAPIQQLADKISGYFVPFIIIISVVTLVTWIIIGFVNFDIIIKYFPSYSKNISK
TEVIIRVAFQTSITVLSIACPCALGLATPTAVMVGTGVAAQNGILIKGGEPLEMAHKIKAVMFDKTGTITHGVPKVMRVL
LLGDVVKMPLKRMLAVVGTAEASSEHPLGMAVTKYCKEELGTELLGYCTDFQAVPGCGISCKVNNIESVLVQNEEGLNEQ
NSYRNSLIGTTDSSLIITPELLGAQAPLAHTVLIGNREWMRRNGLHISTDVDEAMSSHEMKGQTAVLVAIDGELCGMIAI
ADTVKQEAALAVHTLKSMGIDVVLITGDNRKTAKAIATQVGIKKVFAEVLPSHKVAKVQALQSDNKRVAMVGDGVNDSPA
LARADVGIAIGTGTDVAIEAADIVLIRNDLLDVVASIHLSKRTVRRIRLNFVFALIYNLLGIPIAAGVFMPAGLVLQPWM
GSAAMAASSVSVVLSSLQLKCYRKPDSDRYEARAQGHMKPLTPSQISVHIGMDDRWRDLPKTKAWDQISYISQVSRASQK
PKRHGSLVEQQDKWSLLINETHEDQMI</string>
                    <external_references type="UNIPROTKB">A0A6I8R0A5</external_references>
                </sequence>
                <ec_number>7.2.2.8</ec_number>
            </protein_or_peptide>
            <ligand macromolecule_id="2">
                <name>MAGNESIUM ION</name>
                <molecular_weight>
                    <theoretical units="MDa">2.4305e-05</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <formula>MG</formula>
            </ligand>
            <ligand macromolecule_id="3">
                <name>TETRAFLUOROALUMINATE ION</name>
                <molecular_weight>
                    <theoretical units="MDa">0.000102975</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <formula>ALF</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">7</concentration>
                    <buffer>
                        <ph>7.0</ph>
                        <component>
                            <concentration units="mM">20.0</concentration>
                            <name>HEPES</name>
                        </component>
                        <component>
                            <concentration units="mM">150.0</concentration>
                            <formula>NaCl</formula>
                        </component>
                        <component>
                            <concentration units="mM">5.0</concentration>
                            <formula>MgCl2</formula>
                        </component>
                        <component>
                            <concentration units="mM">10.0</concentration>
                            <formula>NaF</formula>
                        </component>
                        <component>
                            <concentration units="mM">0.5</concentration>
                            <name>ADP</name>
                        </component>
                        <component>
                            <concentration units="mM">1.0</concentration>
                            <formula>AlCl3</formula>
                        </component>
                        <component>
                            <concentration units="micromolar">40.0</concentration>
                            <name>GDN</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R1.2/1.3</model>
                        <material>GOLD</material>
                        <mesh>400</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <time units="s">60</time>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">298</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 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>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <coma_free/>
                    </alignment_procedure>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 QUANTUM (4k x 4k)</film_or_detector_model>
                            <detector_mode>SUPER-RESOLUTION</detector_mode>
                            <average_electron_dose_per_image units="e/Å^2">61.0</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>1889296</number_selected>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>CTFFIND</name>
                            <version>1.14</version>
                        </software>
                        <software>
                            <name>cryoSPARC</name>
                            <version>3.2</version>
                        </software>
                    </software_list>
                    <type>PHASE FLIPPING AND AMPLITUDE CORRECTION</type>
                </ctf_correction>
                <startup_model type_of_model="INSILICO MODEL"/>
                <final_reconstruction>
                    <algorithm>FOURIER SPACE</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">3.49</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>3.2</version>
                        </software>
                    </software_list>
                    <number_images_used>118418</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing/>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <details>Iterative heterogeneous classification in cryosparc.</details>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="9617">
        <file>emd_25139.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>179</col>
            <row>111</row>
            <sec>121</sec>
        </dimensions>
        <origin>
            <col>120</col>
            <row>136</row>
            <sec>138</sec>
        </origin>
        <spacing>
            <x>121</x>
            <y>111</y>
            <z>179</z>
        </spacing>
        <cell>
            <a units="Å">102.850006</a>
            <b units="Å">94.350006</b>
            <c units="Å">152.15001</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
        </cell>
        <axis_order>
            <fast>Z</fast>
            <medium>Y</medium>
            <slow>X</slow>
        </axis_order>
        <statistics>
            <minimum>-13.023552</minimum>
            <maximum>19.60285</maximum>
            <average>-0.00000000001225</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">0.85</x>
            <y units="Å">0.8500001</y>
            <z units="Å">0.85</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-25139::::</label>
        <annotation_details>ATP7B State 2</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3RFU</access_code>
                    <chain>
                        <source_name>PDB</source_name>
                        <initial_model_type>experimental model</initial_model_type>
                    </chain>
                </initial_model>
                <refinement_protocol>AB INITIO MODEL</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
