<emd emdb_id="EMD-6453" 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>2015-09-03</deposition>
            <header_release>2015-11-18</header_release>
            <map_release>2016-10-19</map_release>
            <update>2016-10-19</update>
        </key_dates>
        <title>Electron cryo-microscopy of a betanodavirus virus-like particle</title>
        <authors_list>
            <author>Junfeng XIE</author>
            <author>Kunpeng LI</author>
            <author>Yuanzhu GAO</author>
            <author>Runqing HUANG</author>
            <author>Yuxiong LAI</author>
            <author>Yan SHI</author>
            <author>Shaowei YANG</author>
            <author>Guohua ZHU</author>
            <author>Qinfen ZHANG</author>
            <author>Jianguo HE</author>
        </authors_list>
        <keywords>virus-like particle, orange-spotted grouper nervous necrosis virus, betanodavirus</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Junfeng XIE</author>
                    <author order="2">Kunpeng LI</author>
                    <author order="3">Yuanzhu GAO</author>
                    <author order="4">Runqing HUANG</author>
                    <author order="5">Yuxiong LAI</author>
                    <author order="6">Yan SHI</author>
                    <author order="7">Shaowei YANG</author>
                    <author order="8">Guohua ZHU</author>
                    <author order="9">Qinfen ZHANG</author>
                    <author order="10">Jianguo HE</author>
                    <title>Structural analysis and insertion study reveal the ideal sites for surface displaying foreign peptides on virus-like particle of a betanodavirus</title>
                    <journal>To Be Published</journal>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3jbm</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Virus-like particle of orange-spotted grouper nervous necrosis virus generated in E.coli</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Virus-like particle of orange-spotted grouper nervous necrosis virus generated in E.coli</name>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">6.8</theoretical>
                </molecular_weight>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name>Orange-spotted grouper nervous necrosis virus</name>
                <sci_species_name ncbi="421750">Orange-spotted grouper nervous necrosis virus</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="94232">Epinephelus coioides</organism>
                    <synonym_organism>VERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>M15</recombinant_strain>
                    <recombinant_plasmid>pQE30</recombinant_plasmid>
                </host_system>
                <molecular_weight>
                    <theoretical units="MDa">6.8</theoretical>
                </molecular_weight>
                <virus_shell shell_id="1">
                    <diameter units="&#8491;">380</diameter>
                    <triangulation>3</triangulation>
                </virus_shell>
                <virus_type>VIRUS-LIKE PARTICLE</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">
                    <concentration units="mg/mL">1.5</concentration>
                    <buffer>
                        <ph>8.0</ph>
                        <details>PBS buffer</details>
                    </buffer>
                    <grid>
                        <details>300 mesh Quantifoil copper grid with thin carbon support, glow discharged in air atmosphere</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">100</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>blot for 5 min before plunging</method>
                    </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="&#181;m">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.91</nominal_defocus_max>
                    <nominal_magnification>96000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">95</temperature_min>
                        <temperature_max units="K">105</temperature_max>
                        <temperature_average units="K">100</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 200000 times magnification</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <details>Weak beam illumination</details>
                    <date>2011-02-26</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">2.5</sampling_interval>
                            </digitization_details>
                            <number_real_images>1359</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                            <bits_per_pixel>16.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>The particles were selected manually.</details>
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">3.9</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN, JSPR</name>
                        </software>
                    </software_list>
                    <number_images_used>32000</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="432001">
        <file>emd_6453.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>480</col>
            <row>480</row>
            <sec>480</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>480</x>
            <y>480</y>
            <z>480</z>
        </spacing>
        <cell>
            <a units="&#8491;">447.84003</a>
            <b units="&#8491;">447.84003</b>
            <c units="&#8491;">447.84003</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>-9.71350861</minimum>
            <maximum>14.21226978</maximum>
            <average>0.00352491</average>
            <std>0.94922048</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">0.933</x>
            <y units="&#8491;">0.933</y>
            <z units="&#8491;">0.933</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>3.2</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of virus-like particle orange-spotted grouper nervous necrosis virus (OGNNV)</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6453::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>4NWW</access_code>
                </initial_model>
                <software_list>
                    <software>
                        <name>Coot, Phenix</name>
                    </software>
                </software_list>
                <details>Local refinement</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>