<emd emdb_id="EMD-5376" 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>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2011-12-25</deposition>
            <header_release>2012-01-11</header_release>
            <map_release>2012-03-26</map_release>
            <update>2012-10-24</update>
        </key_dates>
        <title>Structure of a transcribing cypovirus by cryo-electron microscopy</title>
        <authors_list>
            <author>Yang C</author>
            <author>Ji G</author>
            <author>Liu H</author>
            <author>Zhang K</author>
            <author>Liu G</author>
            <author>Sun F</author>
            <author>Zhu P</author>
            <author>Cheng L</author>
        </authors_list>
        <keywords>dsRNA virus Reoviridae transcribing cypovirus</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Yang C</author>
                    <author order="2">Ji G</author>
                    <author order="3">Liu H</author>
                    <author order="4">Zhang K</author>
                    <author order="5">Liu G</author>
                    <author order="6">Sun F</author>
                    <author order="7">Zhu P</author>
                    <author order="8">Cheng L</author>
                    <title>Cryo-EM structure of a transcribing cypovirus.</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <volume>109</volume>
                    <first_page>6118</first_page>
                    <last_page>6123</last_page>
                    <year>2012</year>
                    <external_references type="PUBMED">22492979</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1200206109</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3j17</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>transcribing cypovirus</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>transcribing cypovirus</name>
                <number_unique_components>5</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="cypovirus">Bombyx mori cypovirus 1</name>
                <sci_species_name ncbi="110829">Bombyx mori cypovirus 1</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="7091">Bombyx mori</organism>
                    <synonym_organism>INVERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <virus_shell shell_id="1">
                    <diameter units="&#8491;">650</diameter>
                    <triangulation>1</triangulation>
                </virus_shell>
                <virus_type>OTHER</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
                <syn_species_name>cypovirus</syn_species_name>
            </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">
                    <buffer>
                        <ph>8.0</ph>
                    </buffer>
                    <grid>
                        <details>300 mesh quantifoil</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <details>Vitrification instrument: FEI Vitrobot Mark IV</details>
                        <method>blotted for 4s</method>
                    </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_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.8</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.5</nominal_defocus_max>
                    <nominal_magnification>75000.0</nominal_magnification>
                    <calibrated_magnification>125390.0</calibrated_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">92</temperature_average>
                    </temperature>
                    <details>parallel beam</details>
                    <date>2011-07-20</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <number_real_images>845</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">22</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Titan Krios</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>each image</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">4.1</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>IMIRS and ISAF</name>
                        </software>
                    </software_list>
                    <number_images_used>8000</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="729001">
        <file>emd_5376.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>720</col>
            <row>720</row>
            <sec>360</sec>
        </dimensions>
        <origin>
            <col>-360</col>
            <row>-360</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>720</x>
            <y>720</y>
            <z>360</z>
        </spacing>
        <cell>
            <a units="&#8491;">861.12</a>
            <b units="&#8491;">861.12</b>
            <c units="&#8491;">430.56</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>-10.0372839</minimum>
            <maximum>15.12658882</maximum>
            <average>0.0000934</average>
            <std>1.00155878</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.196</x>
            <y units="&#8491;">1.196</y>
            <z units="&#8491;">1.196</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.6</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>This is an image of a surface rendered twofold view of transcribing CPV</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5376::::</details>
    </map>
</emd>