<?xml version='1.0' encoding='utf-8'?>
<emd emdb_id="EMD-22718" version="3.0.2.4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_2_4/emdb.xsd">
    <admin>
        <current_status>
            <date>2021-03-10</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2020-09-26</deposition>
            <header_release>2020-12-16</header_release>
            <map_release>2020-12-16</map_release>
            <update>2021-03-10</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Bill &amp; Melinda Gates Foundation</funding_body>
                <code>OPP1115782</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>nsEM map of the 16055 SOSIP HIV Env trimer in complex with polyclonal Fab from rabbit r2467</title>
        <authors_list>
            <author>Ward AB</author>
            <author>Antanasijevic A</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Brouwer PJM</author>
                    <author order="2">Antanasijevic A</author>
                    <author order="3">de Gast M</author>
                    <author order="4">Allen JD</author>
                    <author order="5">Bijl TPL</author>
                    <author order="6">Yasmeen A</author>
                    <author order="7">Ravichandran R</author>
                    <author order="8">Burger JA</author>
                    <author order="9">Ozorowski G</author>
                    <author order="10">Torres JL</author>
                    <author order="11">LaBranche C</author>
                    <author order="12">Montefiori DC</author>
                    <author order="13">Ringe RP</author>
                    <author order="14">van Gils MJ</author>
                    <author order="15">Moore JP</author>
                    <author order="16">Klasse PJ</author>
                    <author order="17">Crispin M</author>
                    <author order="18">King NP</author>
                    <author order="19">Ward AB</author>
                    <author order="20">Sanders RW</author>
                    <title>Immunofocusing and enhancing autologous Tier-2 HIV-1 neutralization by displaying Env trimers on two-component protein nanoparticles.</title>
                    <journal_abbreviation>Npj Vaccines</journal_abbreviation>
                    <country>UK</country>
                    <volume>6</volume>
                    <first_page>24</first_page>
                    <last_page>24</last_page>
                    <year>2021</year>
                    <external_references type="PUBMED">33563983</external_references>
                    <external_references type="DOI">doi:10.1038/s41541-021-00285-9</external_references>
                    <external_references type="ISSN">2059-0105</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-22718</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>nsEM map of the 16055 SOSIP HIV Env trimer in complex with polyclonal Fab from rabbit r2467 (Week 22)</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>nsEM map of the 16055 SOSIP HIV Env trimer in complex with polyclonal Fab from rabbit r2467 (Week 22)</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="32630">synthetic construct</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
                    <recombinant_strain>HEK293F</recombinant_strain>
                    <recombinant_plasmid>pPPI4</recombinant_plasmid>
                </recombinant_expression>
            </complex_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">
                    <concentration units="mg/mL">0.05</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <component>
                            <concentration units="mM">25.0</concentration>
                            <name>Tris-HCl</name>
                        </component>
                        <component>
                            <concentration units="mM">150.0</concentration>
                            <formula>NaCl</formula>
                            <name>sodium chloride</name>
                        </component>
                        <details>TBS buffer, pH 7.4</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <material>Uranyl Formate</material>
                        <details>Sample diluted to 0.05 mg/mL. 3 uL was applied onto the grid, blotted off, and then stained with 2% uranyl formate for 60 seconds.</details>
                    </staining>
                    <grid>
                        <model>Homemade</model>
                        <material>COPPER</material>
                        <mesh>400</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>CONTINUOUS</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                        </pretreatment>
                    </grid>
                    <details>16055 SOSIP.v8.3 was complexed with the purified polyclonal Fab overnight. The complex was purified using SEC and concentrated. The complex was then diluted in TBS to 0.05mg/ml to be loaded onto an imaging grid.</details>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_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>
                    <c2_aperture_diameter units="µm">100.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">1.5</nominal_defocus_min>
                    <nominal_defocus_max units="µm">1.5</nominal_defocus_max>
                    <nominal_magnification>62000.0</nominal_magnification>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>TVIPS TEMCAM-F416 (4k x 4k)</film_or_detector_model>
                            <number_grids_imaged>1</number_grids_imaged>
                            <average_electron_dose_per_image units="e/Å^2">25.0</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>
                <particle_selection>
                    <number_selected>129971</number_selected>
                </particle_selection>
                <startup_model type_of_model="OTHER">
                    <details>Negative Stain EM map of SOSIP trimer</details>
                </startup_model>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <algorithm>BACK PROJECTION</algorithm>
                    <resolution res_type="BY AUTHOR" units="Å">17.2</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                    <number_images_used>81500</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="44958">
        <file>emd_22718.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>224</col>
            <row>224</row>
            <sec>224</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>224</x>
            <y>224</y>
            <z>224</z>
        </spacing>
        <cell>
            <a units="Å">396.47998</a>
            <b units="Å">396.47998</b>
            <c units="Å">396.47998</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>-0.020700566</minimum>
            <maximum>0.049296938</maximum>
            <average>-6.195533e-05</average>
            <std>0.0027232862</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.7699999</x>
            <y units="Å">1.7699999</y>
            <z units="Å">1.7699999</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.015</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-22718::::</label>
        <annotation_details>nsEM map of the 16055 SOSIP HIV Env trimer in complex with polyclonal Fab from rabbit r2467</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <details>No fitting was performed</details>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>