<?xml version="1.0" encoding="UTF-8"?>
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    <admin>
        <current_status>
            <date>2024-05-15</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2017-03-10</deposition>
            <header_release>2017-03-22</header_release>
            <map_release>2017-06-21</map_release>
            <update>2024-05-15</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Medical Research Council (United Kingdom)</funding_body>
                <code>G1000099</code>
                <country>United Kingdom</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Medical Research Council (United Kingdom)</funding_body>
                <code>G1100525/1</code>
                <country>United Kingdom</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Wellcome Trust</funding_body>
                <code>090532/Z/09/Z</code>
                <country>United Kingdom</country>
            </grant_reference>
        </grant_support>
        <title>CryoEM Structure of Foot and Mouth Disease Virus O PanAsia</title>
        <authors_list>
            <author>Kotecha A</author>
            <author>Stuart D</author>
        </authors_list>
        <keywords>Foot and Mouth Disease Virus, FMDV, virus, OpanAsia</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Kotecha A</author>
                    <author order="2">Wang Q</author>
                    <author order="3">Dong X</author>
                    <author order="4">Ilca SL</author>
                    <author order="5">Ondiviela M</author>
                    <author order="6">Zihe R</author>
                    <author order="7">Seago J</author>
                    <author order="8">Charleston B</author>
                    <author order="9">Fry EE</author>
                    <author order="10">Abrescia NGA</author>
                    <author order="11">Springer TA</author>
                    <author order="12">Huiskonen JT</author>
                    <author order="13">Stuart DI</author>
                    <title>Rules of engagement between alpha v beta 6 integrin and foot-and-mouth disease virus.</title>
                    <journal_abbreviation>Nat Commun</journal_abbreviation>
                    <country>UK</country>
                    <volume>8</volume>
                    <first_page>15408</first_page>
                    <last_page>15408</last_page>
                    <year>2017</year>
                    <external_references type="PUBMED">28534487</external_references>
                    <external_references type="DOI">doi:10.1038/ncomms15408</external_references>
                    <external_references type="ISSN">2041-1723</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>5ned</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Foot and Mouth Disease Virus O PanAsia</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Foot-and-mouth disease virus</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>3</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>4</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <sci_species_name ncbi="12110">Foot-and-mouth disease virus</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="9913">Bos taurus</organism>
                </natural_host>
                <molecular_weight>
                    <theoretical units="MDa">9</theoretical>
                </molecular_weight>
                <virus_shell shell_id="1">
                    <name>Foot and Mouth Disease virus</name>
                    <diameter units="Å">300.0</diameter>
                    <triangulation>3</triangulation>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>SEROTYPE</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
            </virus_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>O PanAsia VP1</name>
                <natural_source database="NCBI">
                    <organism ncbi="12110">Foot-and-mouth disease virus</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.023341467</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="36483">Cricetinae gen. sp.</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>TTSAGESADPVTATVENYGGETQVQRRQHTDVSFILDRFVKVTPKDQINVLDLMQTPAHTLVGALLRTATYYFADLEVAV
KHEGNLTWVPNGAPETALDNTTNPTAYHKAPLTRLALPYTAPHRVLATAYNGNCKYGESHTTNVRGDLQVLAQKAARTLP
TSFNYGAIKATRVTELLYRMKRAETYCPRPLLAIHPSEARHKQKIVAPVKQ</string>
                    <external_references type="UNIPROTKB">A0A1B0SZV3</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>O PanAsia VP2</name>
                <natural_source database="NCBI">
                    <organism ncbi="12110">Foot-and-mouth disease virus</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.024389453000000002</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="36483">Cricetinae gen. sp.</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>DKKTEETTLLEDRILTTRNGHTTSTTQSSVGVTYGYATTEDFVSGPNTSGLETRVVQAERFFKTHLFDWVTSDSFGRCHL
LELPTDHKGVYGSLTDSYAYMRNGWDVEVTAVGNQFNGGCLLVAMVPELCSINKRELYQLTLFPHQFINPRTNMTAHITV
PFVGVNRYDQYKVHKPWTLVVMVVAPLTVNTEGAPQIKVYANIAPTNVHVAGEFPSKE</string>
                    <external_references type="UNIPROTKB">A0A1B0QWS1</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name>O PanAsia VP3</name>
                <natural_source database="NCBI">
                    <organism ncbi="12110">Foot-and-mouth disease virus</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.023938898</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="36483">Cricetinae gen. sp.</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>GIFPVACSDGYGGLVTTDPKTADPAYGKVFNPPRNMLPGRFTNFLDVAEACPTFLRFEGDVPYVTTKTDSDRILAQFDLS
LAAKHMSNTFLAGLAQYYTQYSGTINLHFMFTGPTDAKARYMIAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIP
YLSAADYAYTASDTAETTNVQGWVCLFQITHGKADGDALVVLASAGKDFELRLPVDARTQ</string>
                    <external_references type="UNIPROTKB">J3T9N5</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="4">
                <name>O PanAsia VP4</name>
                <natural_source database="NCBI">
                    <organism ncbi="12110">Foot-and-mouth disease virus</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.008791128</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="36483">Cricetinae gen. sp.</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>GAGQSSPATGSQNQSGNTGSIINNYYMQQYQNSMDTQLGDNAISGGSNEGSTDTTSNHTTNTQNNDWFSKLASSAFSGLF
GALLA</string>
                    <external_references type="UNIPROTKB">E6Y5R5</external_references>
                </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">0.5</concentration>
                    <buffer>
                        <ph>8.0</ph>
                        <component>
                            <concentration units="mM">50.0</concentration>
                            <name>HEPES</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>C-flat-2/1</model>
                        <material>COPPER</material>
                        <mesh>300</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                            <film_thickness>5.0</film_thickness>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <time units="s">15</time>
                            <atmosphere>AIR</atmosphere>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <chamber_temperature units="K">294</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 POLARA 300</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>
                    <c2_aperture_diameter units="µm">50.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.0</nominal_cs>
                    <nominal_defocus_min units="µm">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">4.0</nominal_defocus_max>
                    <nominal_magnification>160000.0</nominal_magnification>
                    <calibrated_magnification>37037.0</calibrated_magnification>
                    <specimen_holder_model>GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <temperature>
                        <temperature_min units="K">70.0</temperature_min>
                        <temperature_max units="K">70.0</temperature_max>
                    </temperature>
                    <alignment_procedure>
                        <basic/>
                    </alignment_procedure>
                    <specialist_optics>
                        <energy_filter>
                            <name>GIF</name>
                            <lower_energy_threshold units="eV">0</lower_energy_threshold>
                            <upper_energy_threshold units="eV">20</upper_energy_threshold>
                        </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>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">3838</width>
                                    <height units="pixel">3710</height>
                                </dimensions>
                                <frames_per_image>2-20</frames_per_image>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>360</number_real_images>
                            <average_exposure_time units="s">5.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">18.0</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>13483</number_selected>
                </particle_selection>
                <startup_model type_of_model="PDB ENTRY">
                    <pdb_model>
                        <pdb_id>1BBT</pdb_id>
                    </pdb_model>
                </startup_model>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>I</point_group>
                    </applied_symmetry>
                    <algorithm>BACK PROJECTION</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">3.1</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>1.3</version>
                        </software>
                    </software_list>
                    <number_images_used>13483</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>COMMON LINE</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>1.3</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>COMMON LINE</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>1.3</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>1.3</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="256001">
        <file>emd_3630.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>400</col>
            <row>400</row>
            <sec>400</sec>
        </dimensions>
        <origin>
            <col>-199</col>
            <row>-200</row>
            <sec>-200</sec>
        </origin>
        <spacing>
            <x>400</x>
            <y>400</y>
            <z>400</z>
        </spacing>
        <cell>
            <a units="Å">540.0</a>
            <b units="Å">540.0</b>
            <c units="Å">540.0</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>-0.16045369</minimum>
            <maximum>0.2585682</maximum>
            <average>0.00020386043</average>
            <std>0.015026387</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.35</x>
            <y units="Å">1.35</y>
            <z units="Å">1.35</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.044</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-3630::::</label>
        <annotation_details>CryoEM Map of FMDV O PanAsia</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <target_criteria>Cross-correlation coefficient</target_criteria>
                <refinement_space>REAL</refinement_space>
                <overall_bvalue>120.0</overall_bvalue>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
