<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-14370" version="3.0.2.8">
    <admin>
        <current_status>
            <date>2022-12-21</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2022-02-17</deposition>
            <header_release>2022-08-24</header_release>
            <map_release>2022-08-24</map_release>
            <update>2022-12-21</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Not funded</funding_body>
            </grant_reference>
        </grant_support>
        <title>Ad-DogTag:DogCatcher-RBD</title>
        <authors_list>
            <author>Dicks MDJ</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Dicks MDJ</author>
                    <author order="2">Rose LM</author>
                    <author order="3">Russell RA</author>
                    <author order="4">Bowman LAH</author>
                    <author order="5">Graham C</author>
                    <author order="6">Jimenez-Guardeno JM</author>
                    <author order="7">Doores KJ</author>
                    <author order="8">Malim MH</author>
                    <author order="9">Draper SJ</author>
                    <author order="10">Howarth M</author>
                    <author order="11">Biswas S</author>
                    <title>Modular capsid decoration boosts adenovirus vaccine-induced humoral immunity against SARS-CoV-2.</title>
                    <journal_abbreviation>Mol.Ther.</journal_abbreviation>
                    <country>US</country>
                    <volume>30</volume>
                    <first_page>3639</first_page>
                    <last_page>3657</last_page>
                    <year>2022</year>
                    <external_references type="PUBMED">35949171</external_references>
                    <external_references type="DOI">doi:10.1016/j.ymthe.2022.08.002</external_references>
                    <external_references type="ISSN">1525-0024</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-14370</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Human adenovirus 5</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Human adenovirus 5</name>
                <parent>0</parent>
                <details>Human adenovirus 5 particle displaying the receptor binding domain (RBD) of SARS CoV-2 spike on the surface of the adenovirus capsid. Adenovirus component produced in HEK293 cells, RBD component produced in CHO-S cells. Components conjugated in vitro using DogTag/DogCatcher protein superglue.</details>
                <sci_species_name ncbi="28285">Human adenovirus 5</sci_species_name>
                <virus_type>VIRION</virus_type>
                <virus_isolate>SEROTYPE</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">
                    <buffer>
                        <ph>7.8</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>TFS GLACIOS</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>
                    <nominal_defocus_min units="µm">2.5</nominal_defocus_min>
                    <nominal_defocus_max units="µm">3.5</nominal_defocus_max>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI FALCON III (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">10.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>I</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">10.5</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                        </software>
                    </software_list>
                    <number_images_used>28307</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="95552">
        <file>emd_14370.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>288</col>
            <row>288</row>
            <sec>288</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>288</x>
            <y>288</y>
            <z>288</z>
        </spacing>
        <cell>
            <a units="Å">1494.72</a>
            <b units="Å">1494.72</b>
            <c units="Å">1494.72</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>-3.888648</minimum>
            <maximum>4.4579563</maximum>
            <average>-0.021553824</average>
            <std>0.56286556</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">5.19</x>
            <y units="Å">5.19</y>
            <z units="Å">5.19</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.3</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-14370::::</label>
        <annotation_details>CryoEM structure of Ad-DogTag:DogCatcher-RBD</annotation_details>
    </map>
</emd>
