<?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-10200">
    <admin>
        <current_status>
            <date>2024-05-22</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-08-07</deposition>
            <header_release>2019-08-21</header_release>
            <map_release>2020-02-12</map_release>
            <update>2024-05-22</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Swedish Research Council</funding_body>
                <code>2018-03387</code>
                <country>Sweden</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Swedish Research Council</funding_body>
                <code>2018-00421</code>
                <country>Sweden</country>
            </grant_reference>
        </grant_support>
        <title>Structure of a marine algae virus of the order Picornavirales</title>
        <authors_list>
            <author>Munke A</author>
            <author>Tomaru Y</author>
        </authors_list>
        <keywords>Picornavirales, Marnaviridae, icosahedral virus, algae virus, jelly roll, VIRUS</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0002-5510-2245" order="1">Munke A</author>
                    <author order="2">Kimura K</author>
                    <author order="3">Tomaru Y</author>
                    <author order="4">Okamoto K</author>
                    <title>Capsid Structure of a Marine Algal Virus of the Order Picornavirales .</title>
                    <journal_abbreviation>J.Virol.</journal_abbreviation>
                    <country>US</country>
                    <volume>94</volume>
                    <year>2020</year>
                    <external_references type="PUBMED">32024776</external_references>
                    <external_references type="DOI">doi:10.1128/JVI.01855-19</external_references>
                    <external_references type="ISSN">1098-5514</external_references>
                    <external_references type="CSD">0825</external_references>
                    <external_references type="ASTM">JOVIAM</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6shl</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Chaetoceros tenuissimus RNA virus type-II</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Chaetoceros tenuissimus RNA virus type-II</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="1516128">Chaetoceros tenuissimus RNA virus type-II</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="426638">Chaetoceros tenuissimus</organism>
                </natural_host>
                <virus_shell shell_id="1">
                    <name>Capsid</name>
                    <triangulation>3</triangulation>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>STRAIN</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>VP1</name>
                <natural_source database="NCBI">
                    <organism ncbi="1516128">Chaetoceros tenuissimus RNA virus type-II</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.029740905999999998</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>DNSNNPVGGNPIDNYGTEHAPLLKEDNQYLVYQGERIVSFKDLLRRYQYLNSYWPQETGSGFRYYTLDSPGMPIYRGWDP
NGIDQGQDSTAGNSPYNFCSMTLLNYLAPAFVCQRGSLRHKWVTAGARVNSTASVLSATRHGVLFPLPLAETAHPLDNAL
VGDRRSELQEMQRSRLNGTAITPVRLNNTLEIELPYYSIGQRFHASRFLDLAGTGDTQGVEIACEISDGGNDANYRLDQF
VSVGEDFTLGMFVGAPIMYFYNDPTAT</string>
                    <external_references type="UNIPROTKB">A0A0B6VJB4</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>VP2</name>
                <natural_source database="NCBI">
                    <organism ncbi="1516128">Chaetoceros tenuissimus RNA virus type-II</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.025911800999999998</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>PSANDGPSFTTSKTSQNTTSENVHFVDGDTPWTYDVAATPDETSKLSGFDDAGLGEFLSRPIKIQQYQWTPGVQLFQTFN
PWSDYFGNADVLEKINRFRNLRCKLCLKVLINGNSFYYGRALLSYNPYLRNDQVTVNRSFFIQDLIAASNKPHILLDPCS
SEGGQMCLPFIWPENYLDITSTGWEDQMGECIIHDFDVLRHANGGTDPITVSIFAWAEDVSLLIPTTVAAQ</string>
                    <external_references type="UNIPROTKB">A0A0B6VJB4</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name>VP3</name>
                <natural_source database="NCBI">
                    <organism ncbi="1516128">Chaetoceros tenuissimus RNA virus type-II</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.028508686000000002</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>SRPAVLSDIQPYVPRYCGNLANSDAPETVNKLSVDSKNELTIDTRTMGLGGADELTIHSIASRMTFWRQFDWPESAVTDT
LLASMSVQPFCIDTVTASPVTEIHSTALAFASAPFETWQGSIKFHFKVVCSEYHRGRLRLVYNPLTNNAGPVAFNQVYST
TIDISNDREFDYECKWTDIRAWNACIGIDGATSATFFNTAAAVTGGTPFDNGTLSVYVVNELATPSTAAADVKVQVWVSA
GDDFAVAVPGVGLSQLSYFQQQ</string>
                    <external_references type="UNIPROTKB">A0A0B6VJB4</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="4">
                <name>VP4</name>
                <natural_source database="NCBI">
                    <organism ncbi="1516128">Chaetoceros tenuissimus RNA virus type-II</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.005406366</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>EFKHDGLISKPASAVAKAADALSMIPYIAPYAKATSMVADKIGKIARIFGY</string>
                    <external_references type="UNIPROTKB">A0A0B6VMZ2</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">
                    <buffer>
                        <ph>7.4</ph>
                    </buffer>
                    <grid>
                        <model>Quantifoil R2/2</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>
                        </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>
                    </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>
                    <nominal_defocus_min units="µm">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">3.0</nominal_defocus_max>
                    <nominal_magnification>140000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <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>COUNTING</detector_mode>
                            <digitization_details/>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>2592</number_real_images>
                            <average_exposure_time units="s">8.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">29.0</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>9920</number_selected>
                </particle_selection>
                <startup_model type_of_model="NONE"/>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>I</point_group>
                    </applied_symmetry>
                    <algorithm>FOURIER SPACE</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>2.1</version>
                        </software>
                    </software_list>
                    <number_images_used>8315</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>NOT APPLICABLE</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>NOT APPLICABLE</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="364501">
        <file>emd_10200.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>450</col>
            <row>450</row>
            <sec>450</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>450</x>
            <y>450</y>
            <z>450</z>
        </spacing>
        <cell>
            <a units="Å">476.99997</a>
            <b units="Å">476.99997</b>
            <c units="Å">476.99997</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>-0.273615</minimum>
            <maximum>0.464667</maximum>
            <average>0.0029608626</average>
            <std>0.027028225</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.06</x>
            <y units="Å">1.06</y>
            <z units="Å">1.06</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.127</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-10200::::</label>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>BACKBONE TRACE</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
