<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_8/emdb.xsd" emdb_id="EMD-0708" version="3.0.1.8">
    <admin>
        <current_status>
            <date>2020-04-08</date>
            <code>REL</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-07-30</deposition>
            <header_release>2020-03-18</header_release>
            <map_release>2020-03-18</map_release>
            <update>2020-04-08</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Science Foundation (China)</funding_body>
                <code>81622031</code>
                <country>China</country>
            </grant_reference>
        </grant_support>
        <title>Apo Machupo virus polymerase homodimer</title>
        <authors_list>
            <author>Peng R</author>
            <author>Xu X</author>
            <author>Jing J</author>
            <author>Peng Q</author>
            <author>Gao GF</author>
            <author>Shi Y</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Peng R</author>
                    <author order="2">Xu X</author>
                    <author order="3">Jing J</author>
                    <author order="4">Wang M</author>
                    <author order="5">Peng Q</author>
                    <author order="6">Liu S</author>
                    <author order="7">Wu Y</author>
                    <author order="8">Bao X</author>
                    <author order="9">Wang P</author>
                    <author order="10">Qi J</author>
                    <author order="11">Gao GF</author>
                    <author order="12">Shi Y</author>
                    <title>Structural insight into arenavirus replication machinery.</title>
                    <journal_abbreviation>Nature</journal_abbreviation>
                    <country>UK</country>
                    <volume>579</volume>
                    <first_page>615</first_page>
                    <last_page>619</last_page>
                    <year>2020</year>
                    <external_references type="PUBMED">32214249</external_references>
                    <external_references type="DOI">doi:10.1038/s41586-020-2114-2</external_references>
                    <external_references type="ISSN">1476-4687</external_references>
                    <external_references type="CSD">0006</external_references>
                    <external_references type="ASTM">NATUAS</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-0708</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Machupo virus polymerase</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Machupo virus polymerase</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="11628">Machupo mammarenavirus</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="2449148">Spodoptera aff. frugiperda 1 BOLD-2017</recombinant_organism>
                    <recombinant_cell>HiFive</recombinant_cell>
                </recombinant_expression>
                <molecular_weight>
                    <experimental units="MDa">0.5</experimental>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Machupo virus polymerase</name>
                <natural_source database="NCBI">
                    <organism ncbi="11628">Machupo mammarenavirus</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="2449148">Spodoptera aff. frugiperda 1 BOLD-2017</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MDEYVQELKGLIRKHIPERCEFGHQKVTFLSQVHPSPLLTEGFKLLSSLVELESCEAHACQANTDQRFVDVILSDNGILCPTLPKVIPDGFKLTGKTLILLETFVRVNPDEFEKKWKADMSKLLNLKHDLQKSGVTLVPIVDGRSNYNNRFVADWVIERIRWLLIEILKASKSMLEIDIEDQEYQRLIHSLSNVKNQSLGLENLEHLKRNSLDYDERLNESLFIGLKGDIRESTVREELIKLKLWFKDEVFSKGLGKFKLTDRRELLESLSSLGAHLDSDVSSCPFCNNKLMEIVYNVTFSCVERTDGVATVDQQFSTTHSNIEKHYLSVLSLCNKIKGLKVFNTRRNTLLFLDLIMVNLMVDISDSCQDAIESLRKSGLIVGQMVMLVNDRVLDILEAVKLIRKKIGTNPNWVKNCSKILERSHPEIWHHLSTLIKQPDFNSLISIAQHLVSDRPIMRYSVERGSDKICRHKLFQEMSSFEQMRLFKTLSSISLSLINSMKTSFSSRLLVNEREFSKYFGNVRLRECYAQRFYLAESLVGFLFYQKTGERSRCYSVYLSDNGVMSEQGSFYCDPKRFFLPVFSDEVLAGMCEEMTSWLDFDTGLMNDTGPILRLLVLAILCSPSKRNQTFLQGLRYFLMAFANQIHHIDLTSKLVVECKSSSEVVVQRLAVGLFIRLLSGESDASLFFSRRFKYLLNVSYLCHLITKETPDRLTDQIKCFEKFIEPKVKFGCAVVNPSLNGKLTVDQEDIMINGLKKFFSKSLRDTEDVQTPGVCKELLNYCVSLFNRGKLKVSGELKNNPFRPNITSTALDLSSNKSVVIPKLDELGNILSTYDKEKLVSACVSSMAERFKTKGRYNLDPDSTDYLILKNLTGLVSAGPKAKSTQEELSLMYEALTEEQVESFNEIKHDVQVALAKMADNSVNTRTKNLGRADNSVKNGNNPLDNLWSPFGVMKEIRAEVSLHEVKDFDPDVLPPEVYKELCDAVYKSSEKCNFFLEGVLDVCPLGLLLKNLTTSSYVDEEYFMCFKYLLIQGHFDQKLGSYEHKSRSRLGFTDETLRLKDEVRLSIRESNSEAIADKLDKSYFTNAALRNLCFYSEDSPTEFTSISSNSGNLKFGLSYKEQVGSNRELYVGDLNTKLMTRLVEDFSEAVGNSMKYTCLNSEKEFERAICDMKMAVNNGDLSCSYDHSKWGPTMSPALFLALLQMLELRTPVDRSKIDLDSVKSILKWHLHKVVEVPINVAEAYCIGKLKRSLGLMGCGSTSLSEEFFHQTMQLNGQIPSHIMSVLDMGQGILHNTSDLYGLITEQFLCYALDLLYDVIPVSYTSSDDQITLIKTPSLDIEGGSDAAEWLEMICFHEFLSSKLNKFVSPKSVIGTFVAEFKSRFFVMGEETPLLTKFVAAALHNVKCKTPTQLSETIDTICDQCIANGVSTKIVTRISKRVNQLIRYSGYGETPFGAIEDQDVKDWVDGSRGYRLQRKIEAIFHDDKETSFIRNCARKVFNDIKRGRIFEENLINLIGRGGDEALTGFLQYAGCSEQEVNRVLNYRWVNLSSFGDLRLVLRTKLMTSRRVLEREEVPTLIKTLQSKLSRNFTKGVKKILAESINKSAFQSSVASGFIGFCKSMGSKCVRDGKGGFLYIKEVYSGVSACTCEICALKPKIIYCNNSLNKVSQFSKPILWDYFSLVLTNACELGEWVFSTVKEPQKPLVLNNQNFFWAVKPKVVRQIEDQLGMNHVLQSIRRNYPVLFDEHLTPFMNDLQVSRTMDSGRLKFLDVCIALDMMNENLGIISHLLKTRDNSVYIVKQSDCALAHIRQSSYTDWELGLSPQQICTNFKTQLVLSSMVNPLVLSTSCLKSFFWFNEVLELEDDSQIELAELTDFALMVKNQNVSRAMFVEDIAMGYVVSNFEGVRISLSNVMVDGVQLPPQEKAPDIGELFGLKAENVIVGLVVQIDHVRMSTKFKLKRKMVYSFSLECIMDVGEIQNKEVILKVVAVDQSVSGSGGNHMLLDGVSVVASLPLFTGQASFDLAAMLIESNLAGSNDNFLMRNVTLDLGGFSPELSDKYSYRLSGPENQEDPLVLKDGAFYVGGERLSTYKVEFTGDLVVKALGALEDDESVVSMLHQLWPYLKATSQVILFQQEDFTIVHDLYKKQLTKSIESFGEWIEFTNFKVAYSKSLKELVISDTQGSFRLKGVMCRPLASTPQVEDIE</string>
                </sequence>
            </protein_or_peptide>
        </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">1.0</concentration>
                    <buffer>
                        <ph>8</ph>
                    </buffer>
                    <grid>
                        <model>Quantifoil R1.2/1.3</model>
                        <material>COPPER</material>
                        <mesh>300</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <atmosphere>AIR</atmosphere>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">277</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <details></details>
                    </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>
                    <specialist_optics>
                        <energy_filter>
                            <name>GIF Bioquantum</name>
                            <slit_width units="eV">20</slit_width>
                        </energy_filter>
                    </specialist_optics>
                    <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>
                            <average_electron_dose_per_image units="e/Å^2">60.0</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>1000000</number_selected>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>Gctf</name>
                            <version>0.50</version>
                        </software>
                    </software_list>
                </ctf_correction>
                <startup_model type_of_model="EMDB MAP">
                    <emdb_id>EMD-0707</emdb_id>
                </startup_model>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <algorithm>FOURIER SPACE</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">7.4</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>25000</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="13501">
        <file>emd_0708.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>150</col>
            <row>150</row>
            <sec>150</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>150</x>
            <y>150</y>
            <z>150</z>
        </spacing>
        <cell>
            <a units="Å">408.0</a>
            <b units="Å">408.0</b>
            <c units="Å">408.0</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>-0.21302661</minimum>
            <maximum>0.5085232</maximum>
            <average>0.0011143158</average>
            <std>0.014782983</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">2.72</x>
            <y units="Å">2.72</y>
            <z units="Å">2.72</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.09</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-0708::::</label>
        <annotation_details>apo Machupo virus polymerase homodimer</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
                <target_criteria>Correlation coefficient</target_criteria>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
