<?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-10142">
    <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>2019-07-24</deposition>
            <header_release>2019-10-02</header_release>
            <map_release>2019-10-02</map_release>
            <update>2024-05-22</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Biotechnology and Biological Sciences Research Council</funding_body>
                <code>BB/R00160X/1</code>
                <country>United Kingdom</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Wellcome Trust</funding_body>
                <code>108466/Z/15/Z</code>
                <country>United Kingdom</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Biotechnology and Biological Sciences Research Council</funding_body>
                <code>BB/L014130/1</code>
                <country>United Kingdom</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Biotechnology and Biological Sciences Research Council</funding_body>
                <code>BB/J004596/1</code>
                <country>United Kingdom</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Biotechnology and Biological Sciences Research Council</funding_body>
                <code>BBS/E/000PR9794</code>
                <country>United Kingdom</country>
            </grant_reference>
        </grant_support>
        <title>Cryo-EM Structure of Barley Yellow Dwarf Virus VLP</title>
        <authors_list>
            <author>Byrne MJ</author>
            <author>Ranson NA</author>
        </authors_list>
        <keywords>Luteovirus, VLP, Capsid., VIRUS LIKE PARTICLE</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Byrne MJ</author>
                    <author order="2">Steele JFC</author>
                    <author order="3">Hesketh EL</author>
                    <author order="4">Walden M</author>
                    <author order="5">Thompson RF</author>
                    <author order="6">Lomonossoff GP</author>
                    <author order="7">Ranson NA</author>
                    <title>Combining Transient Expression and Cryo-EM to Obtain High-Resolution Structures of Luteovirid Particles.</title>
                    <journal_abbreviation>Structure</journal_abbreviation>
                    <country>UK</country>
                    <volume>27</volume>
                    <first_page>1761</first_page>
                    <year>2019</year>
                    <external_references type="PUBMED">31611039</external_references>
                    <external_references type="DOI">doi:10.1016/j.str.2019.09.010</external_references>
                    <external_references type="ISSN">0969-2126</external_references>
                    <external_references type="CSD">2005</external_references>
                    <external_references type="ASTM">STRUE6</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6scl</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Barley yellow dwarf virus</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Barley yellow dwarf virus</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <sci_species_name ncbi="12037">Barley yellow dwarf virus</sci_species_name>
                <virus_type>VIRUS-LIKE PARTICLE</virus_type>
                <virus_isolate>SPECIES</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>true</virus_empty>
            </virus_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Coat protein</name>
                <natural_source database="NCBI">
                    <organism ncbi="12037">Barley yellow dwarf virus</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.022083176</theoretical>
                </molecular_weight>
                <number_of_copies>3</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="4100">Nicotiana benthamiana</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MNSVGRRGPRRANQNGTRRRRRRTVRPVVVVQPNRAGPRRRNGRRKGRGGANFVFRPTGGTEVFVFSVDNLKANSSGAIK
FGPSLSQCPALSDGILKSYHRYKITSIRVEFKSHASANTAGAIFIELDTACKQSALGSYINSFTISKTASKTFRSEAING
KEFQESTIDQFWMLYKANGTTTDTAGQFIITMSVSLMTAK</string>
                    <external_references type="UNIPROTKB">O56812</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>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                    </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>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI FALCON III (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">63.2</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>
                <startup_model type_of_model="INSILICO MODEL"/>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>I</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">3.0</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>324235</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="226493">
        <file>emd_10142.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>384</col>
            <row>384</row>
            <sec>384</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>384</x>
            <y>384</y>
            <z>384</z>
        </spacing>
        <cell>
            <a units="Å">408.96002</a>
            <b units="Å">408.96002</b>
            <c units="Å">408.96002</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>-0.19003971</minimum>
            <maximum>0.27505687</maximum>
            <average>0.0024278294</average>
            <std>0.016245374</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.065</x>
            <y units="Å">1.065</y>
            <z units="Å">1.065</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.06</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-10142::::</label>
        <annotation_details>Electron density map for Barley Yellow Dwarf Virus VLP.</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>BACKBONE TRACE</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
