<emd emdb_id="EMD-6322" version="3.0.1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_1/emdb_relaxed.xsd">
    <admin>
        <current_status>
            <code>REL</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2015-04-21</deposition>
            <header_release>2015-06-10</header_release>
            <map_release>2015-10-28</map_release>
            <update>2015-10-28</update>
        </key_dates>
        <title>Genome and RdRp structure within the capsid of no-transcribing cypovirus</title>
        <authors_list>
            <author>Liu H</author>
            <author>Cheng L</author>
        </authors_list>
        <keywords>non-transcribing cypovirus, RNA-dependent RNA polymerase, genome structure, dsRNA virus</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Liu H</author>
                    <author order="2">Cheng L</author>
                    <title>Cryo-EM shows the polymerase structures and a nonspooled genome within a dsRNA virus</title>
                    <journal>SCIENCE</journal>
                    <volume>349</volume>
                    <first_page>1347</first_page>
                    <last_page>1350</last_page>
                    <year>2015</year>
                    <external_references type="PUBMED">26383954</external_references>
                    <external_references type="DOI">doi:10.1126/science.aaa4938</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3ja5</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>non-transcribing cypovirus</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>non-transcribing cypovirus</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name>Bombyx mori cypovirus 1</name>
                <sci_species_name ncbi="110829">Bombyx mori cypovirus 1</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>VERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <virus_shell shell_id="1">
                    <diameter units="&#8491;">715</diameter>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>SPECIES</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
            </virus_supramolecule>
        </supramolecule_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">
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <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>OTHER</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <nominal_magnification>75000.0</nominal_magnification>
                    <calibrated_magnification>125390.0</calibrated_magnification>
                    <specimen_holder_model>GATAN HELIUM</specimen_holder_model>
                    <date>2010-04-10</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Symmetry-mismatch reconstruction of icosahedral with D3 symmetry imposed</details>
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">12.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>MRC</name>
                        </software>
                    </software_list>
                    <number_images_used>28000</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="105470">
        <file>emd_6322.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>300</col>
            <row>300</row>
            <sec>300</sec>
        </dimensions>
        <origin>
            <col>-150</col>
            <row>-150</row>
            <sec>-150</sec>
        </origin>
        <spacing>
            <x>300</x>
            <y>300</y>
            <z>300</z>
        </spacing>
        <cell>
            <a units="&#8491;">717.6</a>
            <b units="&#8491;">717.6</b>
            <c units="&#8491;">717.6</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>-34.171424870000003</minimum>
            <maximum>50.603507999999998</maximum>
            <average>3.75621819</average>
            <std>13.5210762</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.392</x>
            <y units="&#8491;">2.392</y>
            <z units="&#8491;">2.392</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>22.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Genome and RdRp structures of non-transcribing cypovirus imposed D3 symmetry</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6322::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_6322.jpg</file>
            </figure>
        </figure_list>
        <segmentation_list>
            <segmentation>
                <file>emd_6322_msk_2.map</file>
                <mask_details format="CCP4" size_kbytes="20001">
                    <file>emd_6322_msk_2.map</file>
                    <symmetry>
                        <space_group>1</space_group>
                    </symmetry>
                    <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                    <dimensions>
                        <col>160</col>
                        <row>160</row>
                        <sec>200</sec>
                    </dimensions>
                    <origin>
                        <col>60</col>
                        <row>-80</row>
                        <sec>90</sec>
                    </origin>
                    <spacing>
                        <x>160</x>
                        <y>160</y>
                        <z>200</z>
                    </spacing>
                    <cell>
                        <a units="&#8491;">191.36</a>
                        <b units="&#8491;">191.36</b>
                        <c units="&#8491;">239.2</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>-48.75072479</minimum>
                        <maximum>76.46875</maximum>
                        <average>2.37159181</average>
                        <std>9.694389340000001</std>
                    </statistics>
                    <pixel_spacing>
                        <x units="&#8491;">1.196</x>
                        <y units="&#8491;">1.196</y>
                        <z units="&#8491;">1.196</z>
                    </pixel_spacing>
                    <annotation_details>a RdRp complexe under a fivefold turret at ~6 angstrom resolution (masked from the full density map with D3 symmetry imposed)</annotation_details>
                    <details>::::EMDATABANK.org::::</details>
                </mask_details>
            </segmentation>
            <segmentation>
                <file>emd_6322_msk_1.map</file>
                <mask_details format="CCP4" size_kbytes="2849">
                    <file>emd_6322_msk_1.map</file>
                    <symmetry>
                        <space_group>1</space_group>
                    </symmetry>
                    <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                    <dimensions>
                        <col>90</col>
                        <row>90</row>
                        <sec>90</sec>
                    </dimensions>
                    <origin>
                        <col>60</col>
                        <row>-30</row>
                        <sec>105</sec>
                    </origin>
                    <spacing>
                        <x>90</x>
                        <y>90</y>
                        <z>90</z>
                    </spacing>
                    <cell>
                        <a units="&#8491;">107.64</a>
                        <b units="&#8491;">107.64</b>
                        <c units="&#8491;">107.64</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>-22.414630890000002</minimum>
                        <maximum>44.121860499999997</maximum>
                        <average>1.36205161</average>
                        <std>4.55270624</std>
                    </statistics>
                    <pixel_spacing>
                        <x units="&#8491;">1.196</x>
                        <y units="&#8491;">1.196</y>
                        <z units="&#8491;">1.196</z>
                    </pixel_spacing>
                    <annotation_details>structure of the masked RdRp at ~4.8 angstrom resolution (with D3 symmetry imposed)</annotation_details>
                    <details>::::EMDATABANK.org::::</details>
                </mask_details>
            </segmentation>
        </segmentation_list>
    </interpretation>
</emd>
