<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_4/emdb.xsd" emdb_id="EMD-7513" version="3.0.1.4">
    <admin>
        <current_status>
            <date>2019-05-15</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2018-03-02</deposition>
            <header_release>2018-04-11</header_release>
            <map_release>2019-01-09</map_release>
            <update>2019-05-15</update>
        </key_dates>
        <title>Subtomogram average of mature CHIKV virion budded from human cells</title>
        <authors_list>
            <author>Galaz-Montoya JG</author>
            <author>Jin J</author>
            <author>Sherman MB</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Jin J</author>
                    <author order="2">Galaz-Montoya JG</author>
                    <author order="3">Sherman MB</author>
                    <author order="4">Sun SY</author>
                    <author order="5">Goldsmith CS</author>
                    <author order="6">O'Toole ET</author>
                    <author order="7">Ackerman L</author>
                    <author order="8">Carlson LA</author>
                    <author order="9">Weaver SC</author>
                    <author order="10">Chiu W</author>
                    <author order="11">Simmons G</author>
                    <title>Neutralizing Antibodies Inhibit Chikungunya Virus Budding at the Plasma Membrane.</title>
                    <journal_abbreviation>Cell Host Microbe</journal_abbreviation>
                    <country>US</country>
                    <volume>24</volume>
                    <first_page>417</first_page>
                    <last_page>428.e5</last_page>
                    <year>2018</year>
                    <external_references type="PUBMED">30146390</external_references>
                    <external_references type="DOI">doi:10.1016/j.chom.2018.07.018</external_references>
                    <external_references type="ISSN">1934-6069</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-7513</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Chikungunya virus</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Chikungunya virus</name>
                <parent>0</parent>
                <sci_species_name ncbi="37124">Chikungunya virus</sci_species_name>
                <sci_species_strain>vaccine strain 181/clone 25</sci_species_strain>
                <natural_host database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <strain>vaccine strain 181/clone 25</strain>
                </natural_host>
                <virus_shell shell_id="1">
                    <diameter units="Å">698.0</diameter>
                    <triangulation>4</triangulation>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>true</virus_enveloped>
                <virus_empty>false</virus_empty>
            </virus_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>subtomogramAveraging</method>
            <aggregation_state>cell</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <ph>7.0</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <details></details>
                    </vitrification>
                    <details>CHIKV vaccine strain 181/clone 25 infected U2OS cells.</details>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_microscopy microscopy_id="1">
                    <microscope>JEOL 2200FS</microscope>
                    <illumination_mode>OTHER</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <specialist_optics>
                        <energy_filter>
                            <name>In-column Omega Filter</name>
                            <lower_energy_threshold units="eV">0</lower_energy_threshold>
                            <upper_energy_threshold units="eV">20</upper_energy_threshold>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>DIRECT ELECTRON DE-20 (5k x 3k)</film_or_detector_model>
                            <average_exposure_time units="s">0.6</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">1.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </subtomogram_averaging_microscopy>
            </microscopy_list>
            <subtomogram_averaging_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <details>IMOD was used to align the tiltseries. ICON-GPU was used to reconstruct the aligned tiltseries into tomograms.</details>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">34.0</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN2</name>
                            <version>2.21</version>
                        </software>
                    </software_list>
                    <number_subtomograms_used>35</number_subtomograms_used>
                </final_reconstruction>
                <extraction>
                    <number_tomograms>20</number_tomograms>
                    <number_images_used>47</number_images_used>
                    <software_list>
                        <software>
                            <name>EMAN2</name>
                            <version>2.21</version>
                        </software>
                    </software_list>
                </extraction>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>EMAN2</name>
                            <version>2.21</version>
                        </software>
                    </software_list>
                    <details>Not all images were CTF corrected; only those images and those tiltseries with clear CTF ripples in the power spectrum.</details>
                </ctf_correction>
                <final_angle_assignment>
                    <type>OTHER</type>
                    <software_list>
                        <software>
                            <name>EMAN2</name>
                            <version>2.21</version>
                        </software>
                    </software_list>
                    <details>Self-symmetry search was used to create an initial model. All particles were iterative refined in 3D against such model.</details>
                </final_angle_assignment>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="23329">
        <file>emd_7513.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>180</col>
            <row>180</row>
            <sec>180</sec>
        </dimensions>
        <origin>
            <col>-919</col>
            <row>-919</row>
            <sec>-33</sec>
        </origin>
        <spacing>
            <x>180</x>
            <y>180</y>
            <z>180</z>
        </spacing>
        <cell>
            <a units="Å">1288.7999</a>
            <b units="Å">1288.7999</b>
            <c units="Å">1288.7999</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>0.0</minimum>
            <maximum>12.174003000000001</maximum>
            <average>0.18559761</average>
            <std>0.9999999</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">7.1599994</x>
            <y units="Å">7.1599994</y>
            <z units="Å">7.1599994</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-7513::::</label>
        <annotation_details>Mature CHIKV virion budded from human cells</annotation_details>
    </map>
</emd>
