<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-6401" version="3.0.1.9">
    <admin>
        <status_history_list>
            <status status_id="1">
                <code>HPUB</code>
            </status>
        </status_history_list>
        <current_status>
            <code>OBS</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2015-07-29</deposition>
            <header_release>2015-08-19</header_release>
            <obsolete>2015-10-28</obsolete>
            <update>2015-10-28</update>
        </key_dates>
        <title>In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus</title>
        <authors_list>
            <author>Zhang X</author>
            <author>Ding K</author>
            <author>Yu XK</author>
            <author>Chang W</author>
            <author>Sun JC</author>
            <author>Zhou ZH</author>
        </authors_list>
        <keywords>cryo-EM, dsRNA genome organization, viral polymerase</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Zhang X</author>
                    <author order="2">Ding K</author>
                    <author order="3">Yu X</author>
                    <author order="4">Chang W</author>
                    <author order="5">Sun J</author>
                    <author order="6">Zhou ZH</author>
                    <title>In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus</title>
                    <journal>NATURE</journal>
                    <year>2015</year>
                    <external_references type="DOI">doi:10.1038/nature15767</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>CPV VP4 + polymerase complex (TEC)</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>CPV VP4 + polymerase complex (TEC)</name>
                <number_unique_components>2</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>VP4</name>
                <natural_source database="NCBI">
                    <organism ncbi="110829">Bombyx mori cypovirus 1</organism>
                    <synonym_organism>Cytoplasmic polyhedrosis virus</synonym_organism>
                </natural_source>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI"/>
                <sequence/>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>RNA polymerase</name>
                <natural_source database="NCBI">
                    <organism ncbi="110829">Bombyx mori cypovirus 1</organism>
                    <synonym_organism>Cytoplasmic polyhedrosis virus</synonym_organism>
                </natural_source>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI"/>
                <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>8.0</ph>
                        <details>70 mM Tris-Cl, 10 mM MgCl2, 100 mM NaCl, 2 mM GTP</details>
                    </buffer>
                    <grid>
                        <details>200 mesh Quantifoil holey carbon film</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>FEI VITROBOT MARK II</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_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">0.6</nominal_defocus_min>
                    <nominal_defocus_max units="µm">4.5</nominal_defocus_max>
                    <nominal_magnification>49000.0</nominal_magnification>
                    <calibrated_magnification>49500.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">80</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <electron_beam_tilt_params>0</electron_beam_tilt_params>
                        </legacy>
                    </alignment_procedure>
                    <date>2013-07-26</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN K2 (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="µm">5</sampling_interval>
                            </digitization_details>
                            <number_real_images>4385</number_real_images>
                            <average_electron_dose_per_image units="e/Å^2">25</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">3.3</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Frealign</name>
                        </software>
                    </software_list>
                    <number_images_used>68526</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>1</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="11918">
        <file>emd_6401.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>164</col>
            <row>131</row>
            <sec>142</sec>
        </dimensions>
        <origin>
            <col>-111</col>
            <row>46</row>
            <sec>107</sec>
        </origin>
        <spacing>
            <x>164</x>
            <y>131</y>
            <z>142</z>
        </spacing>
        <cell>
            <a units="Å">132.31</a>
            <b units="Å">165.64</b>
            <c units="Å">143.42</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
        </cell>
        <axis_order>
            <fast>Y</fast>
            <medium>X</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-8.85126591</minimum>
            <maximum>15.05303574</maximum>
            <average>0.0</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.01</x>
            <y units="Å">1.01</y>
            <z units="Å">1.01</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.5</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Averaged CPV VP4 + polymerase</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6401::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_6401.jpg</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>
