<?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-6799">
    <admin>
        <current_status>
            <date>2024-11-06</date>
            <code>REL</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2017-07-16</deposition>
            <header_release>2017-08-09</header_release>
            <map_release>2017-08-09</map_release>
            <update>2024-11-06</update>
        </key_dates>
        <title>PIG GASTRIC H+/K+ - ATPASE IN COMPLEX WITH BYK99</title>
        <authors_list>
            <author>Abe K</author>
            <author>Shimokawa J</author>
        </authors_list>
        <keywords>ion pump, h+, k+-atpase, p-type atpase, membrane protein, Hydrolase, e2, aluminium fluoride, ATP-binding, hydrogen ion transport, ion transport, magnesium, membrane, metal-binding, nucleotide-binding, phosphoprotein, potassium, potassium transport, transmembrane, transport, disulfide bond, glycoprotein, signal-anchor</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Abe K</author>
                    <author order="2">Shimokawa J</author>
                    <author order="3">Naito M</author>
                    <author order="4">Munson K</author>
                    <author order="5">Vagin O</author>
                    <author order="6">Sachs G</author>
                    <author order="7">Suzuki H</author>
                    <author order="8">Tani K</author>
                    <author order="9">Fujiyoshi Y</author>
                    <title>The cryo-EM structure of gastric H(+),K(+)-ATPase with bound BYK99, a high-affinity member of K(+)-competitive, imidazo[1,2-a]pyridine inhibitors</title>
                    <journal_abbreviation>Sci Rep</journal_abbreviation>
                    <country>UK</country>
                    <volume>7</volume>
                    <first_page>6632</first_page>
                    <last_page>6632</last_page>
                    <year>2017</year>
                    <external_references type="PUBMED">28747707</external_references>
                    <external_references type="DOI">doi:10.1038/s41598-017-06698-8</external_references>
                    <external_references type="ISSN">2045-2322</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>5y0b</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>PIG GASTRIC H+/ K+ - ATPASE IN COMPLEX WITH BYK99</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>PIG GASTRIC H+/ K+ - ATPASE IN COMPLEX WITH BYK99</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="9823">Sus scrofa</organism>
                    <tissue>stomach</tissue>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Potassium-transporting ATPase alpha chain 1</name>
                <natural_source database="NCBI">
                    <organism ncbi="9823">Sus scrofa</organism>
                    <tissue>STOMACH</tissue>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.11439968799999999</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MGKAENYELYQVELGPGPSGDMAAKMSKKKAGRGGGKRKEKLENMKKEMEINDHQLSVAELEQKYQTSATKGLSASLAAE
LLLRDGPNALRPPRGTPEYVKFARQLAGGLQCLMWVAAAICLIAFAIQASEGDLTTDDNLYLALALIAVVVVTGCFGYYQ
EFKSTNIIASFKNLVPQQATVIRDGDKFQINADQLVVGDLVEMKGGDRVPADIRILQAQGRKVDNSSLTGESEPQTRSPE
CTHESPLETRNIAFFSTMCLEGTAQGLVVNTGDRTIIGRIASLASGVENEKTPIAIEIEHFVDIIAGLAILFGATFFIVA
MCIGYTFLRAMVFFMAIVVAYVPEGLLATVTVCLSLTAKRLASKNCVVKNLEAVETLGSTSVICSDKTGTLTQNRMTVSH
LWFDNHIHSADTTEDQSGQTFDQSSETWRALCRVLTLCNRAAFKSGQDAVPVPKRIVIGDASETALLKFSELTLGNAMGY
RERFPKVCEIPFNSTNKFQLSIHTLEDPRDPRHVLVMKGAPERVLERCSSILIKGQELPLDEQWREAFQTAYLSLGGLGE
RVLGFCQLYLSEKDYPPGYAFDVEAMNFPTSGLSFAGLVSMIDPPRATVPDAVLKCRTAGIRVIMVTGDHPITAKAIAAS
VGIISEGSETVEDIAARLRVPVDQVNRKDARACVINGMQLKDMDPSELVEALRTHPEMVFARTSPQQKLVIVESCQRLGA
IVAVTGDGVNDSPALKKADIGVAMGIAGSDAAKNAADMILLDDNFASIVTGVEQGRLIFDNLKKSIAYTLTKNIPELTPY
LIYITVSVPLPLGCITILFIELCTDIFPSVSLAYEKAESDIMHLRPRNPKRDRLVNEPLAAYSYFQIGAIQSFAGFTDYF
TAMAQEGWFPLLCVGLRPQWENHHLQDLQDSYGQEWTFGQRLYQQYTCYTVFFISIEMCQIADVLIRKTRRLSAFQQGFF
RNRILVIAIVFQVCIGCFLCYCPGMPNIFNFMPIRFQWWLVPMPFGLLIFVYDEIRKLGVRCCPGSWWDQELYY</string>
                    <external_references type="UNIPROTKB">P19156</external_references>
                </sequence>
                <ec_number>3.6.3.10</ec_number>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>Potassium-transporting ATPase subunit beta</name>
                <natural_source database="NCBI">
                    <organism ncbi="9823">Sus scrofa</organism>
                    <tissue>stomach</tissue>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.033113843999999996</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MAALQEKKSCSQRMEEFQRYCWNPDTGQMLGRTLSRWVWISLYYVAFYVVMSGIFALCIYVLMRTIDPYTPDYQDQLKSP
GVTLRPDVYGEKGLDISYNVSDSTTWAGLAHTLHRFLAGYSPAAQEGSINCTSEKYFFQESFLAPNHTKFSCKFTADMLQ
NCSGRPDPTFGFAEGKPCFIIKMNRIVKFLPGNSTAPRVDCAFLDQPRDGPPLQVEYFPANGTYSLHYFPYYGKKAQPHY
SNPLVAAKLLNVPRNRDVVIVCKILAEHVSFDNPHDPYEGKVEFKLKIQK</string>
                    <external_references type="UNIPROTKB">P18434</external_references>
                </sequence>
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>electronCrystallography</method>
            <aggregation_state>twoDArray</aggregation_state>
            <specimen_preparation_list>
                <crystallography_preparation preparation_id="1">
                    <concentration units="mg/mL">6.5</concentration>
                    <buffer>
                        <ph>4.8</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>NITROGEN</cryogen_name>
                        <instrument>LEICA KF80</instrument>
                    </vitrification>
                    <details>This sample is 2D crystal.</details>
                </crystallography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <crystallography_microscopy microscopy_id="1">
                    <microscope>JEOL KYOTO-3000SFF</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>KODAK SO-163 FILM</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">8.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <camera_length units="mm">1500</camera_length>
                </crystallography_microscopy>
            </microscopy_list>
            <crystallography_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">6.5</resolution>
                    <resolution_method>DIFFRACTION PATTERN/LAYERLINES</resolution_method>
                    <software_list>
                        <software>
                            <name>MRC</name>
                        </software>
                    </software_list>
                </final_reconstruction>
                <crystal_parameters>
                    <unit_cell>
                        <a units="Å">142.6</a>
                        <b units="Å">112.0</b>
                        <c units="Å">320</c>
                        <c_sampling_length units="Å">320</c_sampling_length>
                        <gamma units="deg">90</gamma>
                    </unit_cell>
                    <plane_group>P 2 21 21</plane_group>
                </crystal_parameters>
                <crystallography_statistics>
                    <number_intensities_measured>59212</number_intensities_measured>
                    <number_structure_factors>4974</number_structure_factors>
                    <fourier_space_coverage>47.100000000000001</fourier_space_coverage>
                    <r_sym>0.469</r_sym>
                    <r_merge>0.469</r_merge>
                    <overall_phase_error>33.1</overall_phase_error>
                    <overall_phase_residual>33.100000000000001</overall_phase_residual>
                    <phase_error_rejection_criteria>0</phase_error_rejection_criteria>
                    <high_resolution units="Å">6.5</high_resolution>
                    <shell_list>
                        <shell shell_id="1">
                            <high_resolution units="Å">6.5</high_resolution>
                            <low_resolution units="Å">200.0</low_resolution>
                            <number_structure_factors>4974</number_structure_factors>
                            <phase_residual>33.100000000000001</phase_residual>
                            <fourier_space_coverage>47.100000000000001</fourier_space_coverage>
                            <multiplicity>11.9</multiplicity>
                        </shell>
                    </shell_list>
                </crystallography_statistics>
            </crystallography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="16630">
        <file>emd_6799.map.gz</file>
        <symmetry>
            <space_group>18</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>289</col>
            <row>137</row>
            <sec>105</sec>
        </dimensions>
        <origin>
            <col>-144</col>
            <row>-68</row>
            <sec>-52</sec>
        </origin>
        <spacing>
            <x>136</x>
            <y>104</y>
            <z>288</z>
        </spacing>
        <cell>
            <a units="Å">142.596</a>
            <b units="Å">111.997604</b>
            <c units="Å">319.9968</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>X</medium>
            <slow>Y</slow>
        </axis_order>
        <statistics>
            <minimum>-0.01762751</minimum>
            <maximum>0.02270848</maximum>
            <average>-0.000006678895</average>
            <std>0.003254603</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.0485</x>
            <y units="Å">1.0769</y>
            <z units="Å">1.1111</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.004</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::D_1300004455::::</label>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <target_criteria>correlation coefficient</target_criteria>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
