<emd emdb_id="EMD-2347" version="3.0.1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_1/emdb_relaxed.xsd">
    <admin>
        <current_status>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2013-03-28</deposition>
            <header_release>2013-04-10</header_release>
            <map_release>2013-07-10</map_release>
            <update>2013-11-06</update>
        </key_dates>
        <title>cryo-EM structure of the NavCt voltage-gated sodium channel</title>
        <authors_list>
            <author>Tsai C-J</author>
            <author>Tani K</author>
            <author>Irie K</author>
            <author>Hiroaki Y</author>
            <author>Shimomura T</author>
            <author>McMillan DG</author>
            <author>Cook GM</author>
            <author>Schertler G</author>
            <author>Fujiyoshi Y</author>
            <author>Li X-D</author>
        </authors_list>
        <keywords>Voltage-gated sodium ion channel, tetrameric ion channel</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Tsai CJ</author>
                    <author order="2">Tani K</author>
                    <author order="3">Irie K</author>
                    <author order="4">Hiroaki Y</author>
                    <author order="5">Shimomura T</author>
                    <author order="6">McMillan DG</author>
                    <author order="7">Cook GM</author>
                    <author order="8">Schertler GF</author>
                    <author order="9">Fujiyoshi Y</author>
                    <author order="10">Li XD</author>
                    <title>Two alternative conformations of a voltage-gated sodium channel.</title>
                    <journal>J.MOL.BIOL.</journal>
                    <volume>425</volume>
                    <first_page>4074</first_page>
                    <last_page>4088</last_page>
                    <year>2013</year>
                    <external_references type="PUBMED">23831224</external_references>
                    <external_references type="DOI">doi:10.1016/j.jmb.2013.06.036</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>4bgn</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>voltage-gated sodium channel</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>voltage-gated sodium channel</name>
                <oligomeric_state>Two tetramers of voltage-gated sodium channel</oligomeric_state>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>voltage-gated sodium channel</name>
                <natural_source database="NCBI">
                    <organism ncbi="296745">Caldalkalibacillus thermarum</organism>
                    <strain>TA2.A1</strain>
                    <cellular_location>Plasma membrane</cellular_location>
                </natural_source>
                <number_of_copies>2</number_of_copies>
                <oligomeric_state>tetramer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="469008">Escherichia coli BL21(DE3)</recombinant_organism>
                    <recombinant_strain>C43</recombinant_strain>
                    <recombinant_plasmid>pTrc99A</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">F5L478</external_references>
                    <external_references type="GO">GO:0005216</external_references>
                    <external_references type="INTERPRO">IPR005821</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">4.0</concentration>
                    <buffer>
                        <ph>9.0</ph>
                        <details>50mM glycine-NaOH pH9.0, 200mM NaCl, 4mM MgCl2, 5% glycerol, 5% methyl-2,4-pentanediol, 1.5mM NaN3</details>
                    </buffer>
                    <grid>
                        <details>molybdenum EM grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>NITROGEN</cryogen_name>
                        <instrument>LEICA KF80</instrument>
                    </vitrification>
                    <details>Crystals grown by dialysis</details>
                    <crystal_formation>
                        <details>Crystals grown by dialysis</details>
                    </crystal_formation>
                </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>
                    <nominal_cs units="mm">1.6</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.91</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.82</nominal_defocus_max>
                    <nominal_magnification>40000.0</nominal_magnification>
                    <calibrated_magnification>39500.0</calibrated_magnification>
                    <specimen_holder_model>JEOL</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">4</temperature_min>
                        <temperature_average units="K">4</temperature_average>
                    </temperature>
                    <date>2010-11-05</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>ZEISS SCAI</scanner>
                                <sampling_interval units="&#181;m">7</sampling_interval>
                            </digitization_details>
                            <number_real_images>77</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                            <bits_per_pixel>14.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Helium cooled, top entry</specimen_holder>
                    <tilt_angle_min>0</tilt_angle_min>
                    <tilt_angle_max>60</tilt_angle_max>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">0</min_angle>
                            <max_angle units="deg">60</max_angle>
                        </axis1>
                    </tilt_series>
                </crystallography_microscopy>
            </microscopy_list>
            <crystallography_processing image_processing_id="1">
                <details>Images were processed using MRC suite</details>
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">9.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>MRC</name>
                        </software>
                    </software_list>
                </final_reconstruction>
                <crystal_parameters>
                    <unit_cell>
                        <a units="&#8491;">115.0</a>
                        <b units="&#8491;">115.0</b>
                        <c units="&#8491;">180.0</c>
                        <gamma units="deg">90.0</gamma>
                        <alpha units="deg">90.0</alpha>
                        <beta units="deg">90.0</beta>
                    </unit_cell>
                    <plane_group>P 4</plane_group>
                </crystal_parameters>
                <ctf_correction>
                    <details>Each micrographs</details>
                </ctf_correction>
            </crystallography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="959">
        <file>emd_2347.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>55</col>
            <row>55</row>
            <sec>81</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>-40</sec>
        </origin>
        <spacing>
            <x>55</x>
            <y>55</y>
            <z>81</z>
        </spacing>
        <cell>
            <a units="&#8491;">115.0</a>
            <b units="&#8491;">115.0</b>
            <c units="&#8491;">180.0</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
        </cell>
        <axis_order>
            <fast>Y</fast>
            <medium>X</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-5.02710009</minimum>
            <maximum>6.8197999</maximum>
            <average>0.00326918</average>
            <std>0.99271661</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.090909</x>
            <y units="&#8491;">2.090909</y>
            <z units="&#8491;">2.2222223</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.3</level>
                <source>EMDB</source>
            </contour>
        </contour_list>
        <annotation_details>Cryo-EM structure of voltage-gated Na+ channel</annotation_details>
        <details>::::EMDATABANK.org::::EMD-2347::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3RVY</access_code>
                </initial_model>
                <software_list>
                    <software>
                        <name>CNS</name>
                    </software>
                </software_list>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>