<?xml version="1.0" encoding="UTF-8"?>
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    <admin>
        <current_status>
            <date>2020-01-22</date>
            <code>REL</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2018-11-09</deposition>
            <header_release>2019-07-17</header_release>
            <map_release>2019-07-17</map_release>
            <update>2020-01-22</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Ministry of Science and Technology (Taiwan)</funding_body>
                <code>MOST 103-2321-B-001-048, MOST 104-2321-B-001-019, MOST 105-2321-B-001-009, MOST 106-0210-01-15-02, MOST 106-0210-01-15-04, MOST 107-0210-01-19-01, MOST 107-0210-01-19-02</code>
                <country>Taiwan</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Academia Sinica (Taiwan)</funding_body>
                <code>Grand Challenge project, Nanoscience program, Thematic program AS-103-TP-B12</code>
                <country>Taiwan</country>
            </grant_reference>
        </grant_support>
        <title>Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii extra small virus (XSV) VLP</title>
        <authors_list>
            <author>Wang CH</author>
            <author>Lin HH</author>
            <author>Wu YY</author>
            <author>Chang WH</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Wang CH</author>
                    <author order="2">Lin HH</author>
                    <author order="3">Wu YY</author>
                    <author order="4">Chang WH</author>
                    <title>Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii extra small virus (XSV) VLP</title>
                    <journal_abbreviation>To Be Published</journal_abbreviation>
                    <external_references type="CSD">0353</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-9705</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6jja</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Viruses</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Viruses</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <sci_species_name ncbi="10239">Viruses</sci_species_name>
                <sci_species_strain>Taiwan</sci_species_strain>
                <natural_host database="NCBI">
                    <organism ncbi="511693">Escherichia coli BL21</organism>
                </natural_host>
                <host_system database="NCBI">
                    <recombinant_organism ncbi="222557">Macrobrachium rosenbergii nodavirus</recombinant_organism>
                </host_system>
                <molecular_weight>
                    <theoretical units="MDa">1.146</theoretical>
                </molecular_weight>
                <virus_shell shell_id="1">
                    <name>nucleocapsid protein CP17</name>
                    <diameter units="Å">188.0</diameter>
                    <triangulation>1</triangulation>
                </virus_shell>
                <virus_type>VIRUS-LIKE PARTICLE</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
            </virus_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Capsid protein of giant freshwater prawn Macrobrachium rosenbergii extra small virus</name>
                <natural_source database="NCBI">
                    <organism ncbi="222557">Macrobrachium rosenbergii nodavirus</organism>
                    <strain>Taiwan</strain>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="511693">Escherichia coli BL21</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MNKRINNNRRTMRSRRGRGRTMGSNLIPYANSPVPIPYTPPVTPVTVIGNPRKTTWIDIDLSSEESGIYTLTVGSYRNRITKLGPSKPNFIIEKVAAYAAPGDYKVVLNDFKTGIQVVDEGSYAHRAAAGILYPPAAQMFYGISATGTLNTITTTAKDPVPVVRALVTYWDSEQ</string>
                </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">
                    <concentration units="mg/mL">10</concentration>
                    <buffer>
                        <ph>8</ph>
                        <component>
                            <concentration units="mM">50.0</concentration>
                            <formula>Tris</formula>
                        </component>
                        <component>
                            <concentration units="mM">50.0</concentration>
                            <formula>NaCl</formula>
                        </component>
                        <component>
                            <concentration units="mM">1.0</concentration>
                            <formula>CaCl2</formula>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R1.2/1.3</model>
                        <material>COPPER</material>
                        <mesh>200</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY ARRAY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <atmosphere>AIR</atmosphere>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">277</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <details></details>
                    </vitrification>
                    <details>The XSV-VLPs was purified by 10-25% sucrose density gradient</details>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TALOS ARCTICA</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <c2_aperture_diameter units="µm">50.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <calibrated_defocus_min units="µm">0.51</calibrated_defocus_min>
                    <calibrated_defocus_max units="µm">3.03</calibrated_defocus_max>
                    <nominal_magnification>120000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <temperature>
                        <temperature_min units="K">93.0</temperature_min>
                        <temperature_max units="K">103.0</temperature_max>
                    </temperature>
                    <alignment_procedure>
                        <coma_free/>
                    </alignment_procedure>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI FALCON III (4k x 4k)</film_or_detector_model>
                            <detector_mode>INTEGRATING</detector_mode>
                            <number_real_images>998</number_real_images>
                            <average_exposure_time units="s">20.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">100.0</average_electron_dose_per_image>
                            <details>Images were collected in movie-mode with 65 frames within 5 second</details>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <particle_selection>
                    <number_selected>10755</number_selected>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                        <software>
                            <name>Gctf</name>
                        </software>
                    </software_list>
                </ctf_correction>
                <startup_model type_of_model="NONE">
                    <details>ab initio 3D model reconstruction by cryoSPARC</details>
                </startup_model>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>I</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">2.9</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                    <number_images_used>10755</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                        <software>
                            <name>cryoSPARC</name>
                            <version>2</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="131073">
        <file>emd_9705.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>320</col>
            <row>320</row>
            <sec>320</sec>
        </dimensions>
        <origin>
            <col>-159</col>
            <row>-159</row>
            <sec>-159</sec>
        </origin>
        <spacing>
            <x>320</x>
            <y>320</y>
            <z>320</z>
        </spacing>
        <cell>
            <a units="Å">273.6</a>
            <b units="Å">273.6</b>
            <c units="Å">273.6</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>-0.38343602</minimum>
            <maximum>0.58749646</maximum>
            <average>0.0014456568</average>
            <std>0.03443572</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">0.855</x>
            <y units="Å">0.855</y>
            <z units="Å">0.855</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.11</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-9705::::</label>
        <annotation_details>The cryo-EM map of XSV-VLP</annotation_details>
    </map>
</emd>
