<?xml version='1.0' encoding='utf-8'?>
<emd emdb_id="EMD-26174" version="3.0.2.7" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_2_7/emdb.xsd">
    <admin>
        <current_status>
            <date>2022-08-10</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2022-02-12</deposition>
            <header_release>2022-06-01</header_release>
            <map_release>2022-06-01</map_release>
            <update>2022-08-10</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>R01GM108753</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>R35GM122564</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Second class of AAV2 bound with PKD1-2 revealed by classification of aligned subtomgrams</title>
        <authors_list>
            <author>Hu GQ</author>
            <author>Silveria MA</author>
            <author>Chapman MS</author>
            <author>Stagg SM</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Hu G</author>
                    <author order="2">Silveria MA</author>
                    <author order="3">Zane GM</author>
                    <author ORCID="0000-0001-8525-8585" order="4">Chapman MS</author>
                    <author ORCID="0000-0001-8855-4152" order="5">Stagg SM</author>
                    <title>Adeno-Associated Virus Receptor-Binding: Flexible Domains and Alternative Conformations through Cryo-Electron Tomography of Adeno-Associated Virus 2 (AAV2) and AAV5 Complexes.</title>
                    <journal_abbreviation>J.Virol.</journal_abbreviation>
                    <country>US</country>
                    <volume>96</volume>
                    <first_page>e0010622</first_page>
                    <last_page>e0010622</last_page>
                    <year>2022</year>
                    <external_references type="PUBMED">35674430</external_references>
                    <external_references type="DOI">doi:10.1128/jvi.00106-22</external_references>
                    <external_references type="ISSN">1098-5514</external_references>
                    <external_references type="CSD">0825</external_references>
                    <external_references type="ASTM">JOVIAM</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-26174</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Binary complex of AAV-2 with a two domain fragment of its cellular receptor, AAVR</name>
        <supramolecule_list>
            <complex_supramolecule chimera="true" supramolecule_id="1">
                <name>Binary complex of AAV-2 with a two domain fragment of its cellular receptor, AAVR</name>
                <parent>0</parent>
                <molecular_weight>
                    <experimental units="MDa">0.082</experimental>
                </molecular_weight>
            </complex_supramolecule>
            <complex_supramolecule chimera="true" supramolecule_id="2">
                <name>AAV-2</name>
                <parent>1</parent>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Adeno-associated virus - 2</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="7108">Spodoptera frugiperda</recombinant_organism>
                </recombinant_expression>
                <molecular_weight>
                    <theoretical units="MDa">0.060</theoretical>
                </molecular_weight>
            </complex_supramolecule>
            <complex_supramolecule chimera="true" supramolecule_id="3">
                <name>AAVR</name>
                <parent>1</parent>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <molecular_weight>
                    <theoretical units="MDa">0.022</theoretical>
                </molecular_weight>
            </complex_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">
                    <concentration units="mg/mL">0.2</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <component>
                            <concentration units="mM">25.0</concentration>
                            <name>Gibco HEPES</name>
                        </component>
                        <component>
                            <concentration units="mM">150.0</concentration>
                            <formula>NaCl</formula>
                            <name>sodium chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">50.0</concentration>
                            <formula>MgCl2</formula>
                            <name>Magnesium chloride</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R1.2/1.3</model>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                            <film_thickness units="nm">15.0</film_thickness>
                        </support_film>
                    </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>4ul of AAV-2  at concentration 0.2 mg/ml was was applied on grid and incubated for 1.5 minutes. The grid was gently blotted on the side with filter paper, and another 4ul of  PKD1-2 at concentration 1.5 mg/ml was applied and allowed to incubate for another 1.5 minutes followed by plunge-freeze using a Vitrobot Mark IV.. </details>
                    </vitrification>
                    <details>4ul of AAV-2  at concentration 0.2 mg/ml was was applied on grid and incubated for 1.5 minutes. The grid was gently blotted on the side with filter paper, and another 4ul of  PKD1-2 at concentration 1.5 mg/ml was applied and allowed to incubate for another 1.5 minutes followed by plunge-freeze using a Vitrobot Mark IV.</details>
                </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>
                    <c2_aperture_diameter units="µm">100.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">5.0</nominal_defocus_min>
                    <calibrated_defocus_min units="µm">5.0</calibrated_defocus_min>
                    <nominal_defocus_max units="µm">5.0</nominal_defocus_max>
                    <calibrated_defocus_max units="µm">5.0</calibrated_defocus_max>
                    <nominal_magnification>33000.0</nominal_magnification>
                    <calibrated_magnification>33000.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K3 (6k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">5760</width>
                                    <height units="pixel">4092</height>
                                </dimensions>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <average_electron_dose_per_image units="e/Å^2">1.6</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>
                    <number_classes_used>4</number_classes_used>
                    <applied_symmetry>
                        <point_group>C3</point_group>
                    </applied_symmetry>
                    <resolution res_type="BY AUTHOR" units="Å">20.0</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN</name>
                            <version>2</version>
                        </software>
                    </software_list>
                    <number_subtomograms_used>7620</number_subtomograms_used>
                </final_reconstruction>
                <extraction>
                    <number_tomograms>3</number_tomograms>
                    <number_images_used>127</number_images_used>
                    <reference_model>EMD-0553</reference_model>
                    <method>manual picking</method>
                    <software_list>
                        <software>
                            <name>EMAN</name>
                            <version>2</version>
                        </software>
                    </software_list>
                </extraction>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>EMAN</name>
                            <version>2</version>
                        </software>
                    </software_list>
                </ctf_correction>
                <final_three_d_classification>
                    <number_classes>4</number_classes>
                    <software_list>
                        <software>
                            <name>EMAN</name>
                            <version>2</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
                <final_angle_assignment>
                    <type>OTHER</type>
                    <software_list>
                        <software>
                            <name>EMAN</name>
                            <version>2</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="172">
        <file>emd_26174.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>35</col>
            <row>35</row>
            <sec>35</sec>
        </dimensions>
        <origin>
            <col>-17</col>
            <row>-17</row>
            <sec>-17</sec>
        </origin>
        <spacing>
            <x>35</x>
            <y>35</y>
            <z>35</z>
        </spacing>
        <cell>
            <a units="Å">191.8</a>
            <b units="Å">191.8</b>
            <c units="Å">191.8</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>0.21</minimum>
            <maximum>0.765</maximum>
            <average>0.22391513</average>
            <std>0.055821303</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">5.48</x>
            <y units="Å">5.48</y>
            <z units="Å">5.48</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.25</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-26174::::</label>
        <annotation_details>Second class of AAV2 bound with PKD1-2 revealed by classification of aligned subtomgrams</annotation_details>
    </map>
</emd>