<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-25064" version="3.0.3.0">
    <admin>
        <current_status>
            <date>2023-04-19</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2021-09-29</deposition>
            <header_release>2022-10-05</header_release>
            <map_release>2022-10-05</map_release>
            <update>2023-04-19</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health &amp; Human Development (NIH/NICHD)</funding_body>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>in situ SIVmac239-Env trimers on the surface of AT-2-inactivated virions</title>
        <authors_list>
            <author>Liu J</author>
            <author>Wang CY</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0002-3775-6560" order="1">Gorman J</author>
                    <author order="2">Wang C</author>
                    <author order="3">Mason RD</author>
                    <author order="4">Nazzari AF</author>
                    <author order="5">Welles HC</author>
                    <author ORCID="0000-0002-3935-4637" order="6">Zhou T</author>
                    <author ORCID="0000-0003-0662-7843" order="7">Bess Jr JW</author>
                    <author order="8">Bylund T</author>
                    <author ORCID="0000-0002-4972-3811" order="9">Lee M</author>
                    <author ORCID="0000-0002-2159-5248" order="10">Tsybovsky Y</author>
                    <author order="11">Verardi R</author>
                    <author ORCID="0000-0002-0865-4522" order="12">Wang S</author>
                    <author order="13">Yang Y</author>
                    <author order="14">Zhang B</author>
                    <author ORCID="0000-0002-0445-2325" order="15">Rawi R</author>
                    <author ORCID="0000-0002-2381-1151" order="16">Keele BF</author>
                    <author order="17">Lifson JD</author>
                    <author ORCID="0000-0003-3108-6735" order="18">Liu J</author>
                    <author ORCID="0000-0001-7448-7040" order="19">Roederer M</author>
                    <author ORCID="0000-0003-3560-232X" order="20">Kwong PD</author>
                    <title>Cryo-EM structures of prefusion SIV envelope trimer.</title>
                    <journal_abbreviation>Nat.Struct.Mol.Biol.</journal_abbreviation>
                    <country>US</country>
                    <volume>29</volume>
                    <first_page>1080</first_page>
                    <last_page>1091</last_page>
                    <year>2022</year>
                    <external_references type="PUBMED">36344847</external_references>
                    <external_references type="DOI">doi:10.1038/s41594-022-00852-1</external_references>
                    <external_references type="ISSN">1545-9985</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-25064</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Simian immunodeficiency virus</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Simian immunodeficiency virus</name>
                <parent>0</parent>
                <sci_species_name ncbi="11723">Simian immunodeficiency virus</sci_species_name>
                <sci_species_strain>SIVmac239</sci_species_strain>
                <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>particle</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <ph>7.4</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                    </vitrification>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_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>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K3 (6k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">1.2</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>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C3</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">7.0</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <number_subtomograms_used>32857</number_subtomograms_used>
                </final_reconstruction>
                <extraction>
                    <number_tomograms>55</number_tomograms>
                    <number_images_used>40000</number_images_used>
                </extraction>
                <final_angle_assignment>
                    <type>OTHER</type>
                </final_angle_assignment>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="32001">
        <file>emd_25064.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>200</col>
            <row>200</row>
            <sec>200</sec>
        </dimensions>
        <origin>
            <col>-100</col>
            <row>-100</row>
            <sec>-100</sec>
        </origin>
        <spacing>
            <x>200</x>
            <y>200</y>
            <z>200</z>
        </spacing>
        <cell>
            <a units="Å">276.0</a>
            <b units="Å">276.0</b>
            <c units="Å">276.0</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>-0.024806794</minimum>
            <maximum>0.25254935</maximum>
            <average>-1.626936e-11</average>
            <std>0.006167115</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.38</x>
            <y units="Å">1.38</y>
            <z units="Å">1.38</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.01</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-25064::::</label>
        <annotation_details>in situ SIVmac239-Env trimers on the surface of AT-2-inactivated virions</annotation_details>
    </map>
</emd>
