<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-4008" version="3.0.0.1" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_0_1/emdb.xsd">
    <admin>
        <current_status>
            <date>2018-11-28</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2016-06-03</deposition>
            <header_release>2016-06-22</header_release>
            <map_release>2016-06-22</map_release>
            <update>2018-11-28</update>
        </key_dates>
        <title>Structure of the wt PFV glycoprotein from the iNAB Gag mutant by cryo-electron tomography</title>
        <authors_list>
            <author>Effantin G</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Effantin G</author>
                    <author order="2">Estrozi LF</author>
                    <author order="3">Aschman N</author>
                    <author order="4">Renesto P</author>
                    <author order="5">Stanke N</author>
                    <author order="6">Lindemann D</author>
                    <author order="7">Schoehn G</author>
                    <author order="8">Weissenhorn W</author>
                    <title>Cryo-electron Microscopy Structure of the Native Prototype Foamy Virus Glycoprotein and Virus Architecture.</title>
                    <journal_abbreviation>Plos Pathog.</journal_abbreviation>
                    <country>US</country>
                    <volume>12</volume>
                    <first_page>e1005721</first_page>
                    <last_page>e1005721</last_page>
                    <year>2016</year>
                    <external_references type="PUBMED">27399201</external_references>
                    <external_references type="DOI">doi:10.1371/journal.ppat.1005721</external_references>
                    <external_references type="ISSN">1553-7374</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-4008</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
                <details>EMDB-4006 is the wt PFV glycoprotein</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-4007</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>EMDB-4007 is a mutant in env PFV glycoprotein</details>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Human spumaretrovirus</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Human spumaretrovirus</name>
                <parent>0</parent>
                <details>Mutant in the Gag polyprotein</details>
                <sci_species_name ncbi="11963">Human spumaretrovirus</sci_species_name>
                <host_system database="NCBI">
                    <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
                    <recombinant_plasmid>pcoPG4 GR R/A, pcoPE32, pcoPP</recombinant_plasmid>
                </host_system>
                <molecular_weight>
                    <theoretical units="MDa">0.33</theoretical>
                </molecular_weight>
                <virus_type>VIRION</virus_type>
                <virus_isolate>SPECIES</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>7.5</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <details />
                    </vitrification>
                    <details>In the iNAB mutant,23 arginines in the glycine/arginine rich (GR) region in the C-terminus of Gag have been replaced by alanine, which results in a Gag protein unable to bind nucleic acid. Virus particles are still released from cells, although less efficiently, but are non-infectious and display capsid assembly defects.</details>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F20</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>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI EAGLE (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^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>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C3</point_group>
                    </applied_symmetry>
                    <resolution res_type="BY AUTHOR" units="&#8491;">29.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>PEET</name>
                        </software>
                    </software_list>
                    <number_subtomograms_used>3000</number_subtomograms_used>
                </final_reconstruction>
                <extraction>
                    <number_tomograms>5</number_tomograms>
                    <number_images_used>4450</number_images_used>
                </extraction>
                <final_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing />
                    <software_list>
                        <software>
                            <name>PEET</name>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="1373">
        <file>emd_4008.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>70</col>
            <row>70</row>
            <sec>70</sec>
        </dimensions>
        <origin>
            <col>-35</col>
            <row>-35</row>
            <sec>-35</sec>
        </origin>
        <spacing>
            <x>70</x>
            <y>70</y>
            <z>70</z>
        </spacing>
        <cell>
            <a units="&#8491;">532.0</a>
            <b units="&#8491;">532.0</b>
            <c units="&#8491;">532.0</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>-3.2232833</minimum>
            <maximum>3.8961947</maximum>
            <average>0.000000000031544</average>
            <std>1.</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">7.6</x>
            <y units="&#8491;">7.6</y>
            <z units="&#8491;">7.6</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.654</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-4008::::</label>
    </map>
</emd>