<?xml version="1.0" encoding="UTF-8"?>
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    <admin>
        <current_status>
            <date>2024-10-23</date>
            <code>REL</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2017-01-21</deposition>
            <header_release>2017-02-15</header_release>
            <map_release>2017-03-08</map_release>
            <update>2024-10-23</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>the Ministry of Science and Technology of China</funding_body>
                <code>2015CB910101, 2016YFA0500402, 2014ZX09507003-006</code>
                <country>China</country>
            </grant_reference>
            <grant_reference>
                <funding_body>the National Natural Science Foundation of China</funding_body>
                <code>projects 31621092, 31630017, and 31611130036</code>
                <country>China</country>
            </grant_reference>
        </grant_support>
        <title>Structure of a eukaryotic voltage-gated sodium channel at near atomic resolution</title>
        <authors_list>
            <author>Shen H</author>
            <author>Zhou Q</author>
        </authors_list>
        <keywords>ion channel, membrane protein</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Shen H</author>
                    <author order="2">Zhou Q</author>
                    <author order="3">Pan X</author>
                    <author order="4">Li Z</author>
                    <author order="5">Wu J</author>
                    <author order="6">Yan N</author>
                    <title>Structure of a eukaryotic voltage-gated sodium channel at near-atomic resolution.</title>
                    <journal_abbreviation>Science</journal_abbreviation>
                    <country>US</country>
                    <volume>355</volume>
                    <year>2017</year>
                    <external_references type="PUBMED">28183995</external_references>
                    <external_references type="DOI">doi:10.1126/science.aal4326</external_references>
                    <external_references type="ISSN">1095-9203</external_references>
                    <external_references type="CSD">0038</external_references>
                    <external_references type="ASTM">SCIEAS</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>5x0m</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>voltage-gated sodium channel</name>
        <supramolecule_list>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name>voltage-gated sodium channel</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="6978">Periplaneta americana</organism>
                </natural_source>
            </organelle_or_cellular_component_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Sodium channel protein</name>
                <natural_source database="NCBI">
                    <organism ncbi="6978">Periplaneta americana</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.18387542199999998</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MASWSHPQFEKGGGARGGSGGGSWSHPQFEKGFDYKDDDDKGTMADNSPLIREERQRLFRPYTRAMLTAPSAQPAKENGK
TEENKDNSRDKGRGANKDRDGSAHPDQALEQGSRLPARMRNIFPAELASTPLEDFDPFYKNKKTFVVVTKAGDIFRFSGE
KSLWMLDPFTPIRRVAISTMVQPIFSYFIMITILIHCIFMIMPATQTTYILELVFLSIYTIEVVVKVLARGFILHPFAYL
RDPWNWLDFLVTLIGYITLVVDLGHLYALRAFRVLRSWRTVTIVPGWRTIVDALSLSITSLKDLVLLLLFSLFVFAVLGL
QIYMGVLTQKCVKHFPADGSWGNFTDERWFNYTSNSSHWYIPDDWIEYPLCGNSSGAGMCPPGYTCLQGYGGNPNYGYTS
FDTFGWAFLSVFRLVTLDYWEDLYQLALRSAGPWHILFFIIVVFYGTFCFLNFILAVVVMSYTHMVKRADEEKAAERELK
KEKKAASVANNTANGQEQTTIEMNGDEAVVIDNNDQAARQQSDPETPAPSVTQRLTDFLCVWDCCVPWQKLQGAIGAVVL
SPFFELFIAVIIVLNITFMALDHHDMNIEFERILRTGNYIFTSIYIVEAVLKIIALSPKFYFKDSWNVFDFIIVVFAILE
LGLEGVQGLSVFRSFRLLRVFRLAKFWPTLNNFMSVMTKSYGAFVNVMYVMFLLLFIFAIIGMQLFGMNYIDNMERFPDG
DLPRWNFTDFLHSFMIVFRALCGEWIESMWDCMLVGDWSCIPFFVAVFFVGNLVILNLLIALLLNNYGSFCTSPTSDEED
SKDEDALAQIVRIFKRFKPNLNAVKLSPMKPDSEDIVESQEIQGNNIADAEDVLAGEFPPDCCCNAFYKCFPSRPARDSS
VQRMWSNIRRVCFLLAKNKYFQKFVTAVLVITSVLLALEDIYLPQRPVLVNITLYVDYVLTAFFVIEMIIMLFAVGFKKY
FTSKWYWLDFIVVVAYLLNFVLMCAGIEALQTLRLLRVFRLFRPLSKVNGMQVVTSTLVEAVPHIFNVILVGIFFWLVFA
IMGVQLFAGKFYKCVDENSTVLSHEITMDRNDCLHENYTWENSPMNFDHVGNAYLSLLQVATFKGWLQIMNDAIDSREVH
KQPIRETNIYMYLYFIFFIVFGSFFILKLFVCILIDIFRQQRRKAEGLSATDSRTQLIYRRAVMRTMSAKPVKRIPKPTC
HPQSLMYDISVNRKFEYTMMILIILNVAVMAIDHYGQSMEFSEVLDYLNLIFIIIFFVECVIKVSGLRHHYFKDPWNIID
FLYVVLAIAGLMLSDVIEKYFISPTLLRILRILRVGRLLRYFQSARGMRLLLLALRKALRTLFNVSFLLFVIMFVYAVFG
MEFFMHIRDAGAIDDVYNFKTFGQSIILLFQLATSAGWDGVYFAIANEEDCRAPDHELGYPGNCGSRALGIAYLVSYLII
TCLVVINMYAAVILDYVLEVYEDSKEGLTDDDYDMFFEVWQQFDPEATQYIRYDQLSELLEALQPPLQVQKPNKYKILSM
NIPICKDDHIFYKDVLEALVKDVFSRRGSPVEAGDVQAPNVDEAEYKPVSSTLQRQREEYCVRLIQNAWRKHKQQN</string>
                    <external_references type="UNIPROTKB">D0E0C2</external_references>
                </sequence>
            </protein_or_peptide>
            <ligand macromolecule_id="5">
                <name>2-acetamido-2-deoxy-beta-D-glucopyranose</name>
                <molecular_weight>
                    <theoretical units="MDa">0.000221208</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <formula>NAG</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">1</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <details>25 mM Tris-HCl, pH 7.4, 50mM NaCl, 0.1% digitonin, 2.5 mM D-Desthiobiotin and protease inhibitor cocktail</details>
                    </buffer>
                    <grid>
                        <model>Quantifoil R1.2/1.3</model>
                        <material>COPPER</material>
                        <mesh>200</mesh>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">281</chamber_temperature>
                        <details>Grids were blotted for 3.5 s and flash-frozen in liquid ethane cooled by liquid nitrogen.. </details>
                    </vitrification>
                    <details>This sample was monodisperse</details>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</microscope>
                    <illumination_mode>SPOT SCAN</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">2.7</nominal_cs>
                    <calibrated_defocus_min units="µm">1.7</calibrated_defocus_min>
                    <calibrated_defocus_max units="µm">2.6</calibrated_defocus_max>
                    <nominal_magnification>22500.0</nominal_magnification>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>SUPER-RESOLUTION</detector_mode>
                            <digitization_details>
                                <frames_per_image>1-32</frames_per_image>
                            </digitization_details>
                            <average_exposure_time units="s">0.25</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">1.5625</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>4739175</number_selected>
                </particle_selection>
                <startup_model type_of_model="EMDB MAP">
                    <emdb_id>EMD-9513</emdb_id>
                </startup_model>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">3.8</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                    <number_images_used>1373581</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>NOT APPLICABLE</type>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>ANGULAR RECONSTITUTION</type>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="32001">
        <file>emd_6698.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>200</col>
            <row>200</row>
            <sec>200</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>200</x>
            <y>200</y>
            <z>200</z>
        </spacing>
        <cell>
            <a units="Å">258.0</a>
            <b units="Å">258.0</b>
            <c units="Å">258.0</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>-0.26366407</minimum>
            <maximum>0.391851</maximum>
            <average>0.00046030077</average>
            <std>0.014029253</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.29</x>
            <y units="Å">1.29</y>
            <z units="Å">1.29</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0465</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-6698::::</label>
        <annotation_details>overall map</annotation_details>
    </map>
    <interpretation>
        <additional_map_list>
            <additional_map format="CCP4" size_kbytes="32001">
                <file>emd_6698_additional_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>200</col>
                    <row>200</row>
                    <sec>200</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>200</x>
                    <y>200</y>
                    <z>200</z>
                </spacing>
                <cell>
                    <a units="Å">258.0</a>
                    <b units="Å">258.0</b>
                    <c units="Å">258.0</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>-0.48787493</minimum>
                    <maximum>0.706062</maximum>
                    <average>0.00045998665</average>
                    <std>0.024214024</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.29</x>
                    <y units="Å">1.29</y>
                    <z units="Å">1.29</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::D_1300002732::::</label>
                <annotation_details>overall map with B factor of -300</annotation_details>
            </additional_map>
        </additional_map_list>
    </interpretation>
</emd>
