<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://ftp.ebi.ac.uk/pub/databases/em_ebi/emdb_related/emdb-schemas/emdb_schemas/v3/v3_0_9_3/emdb.xsd" version="3.0.9.3" emdb_id="EMD-41977">
    <admin>
        <current_status>
            <date>2024-09-11</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2023-09-15</deposition>
            <header_release>2024-09-11</header_release>
            <map_release>2024-09-11</map_release>
            <update>2024-09-11</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Bill &amp; Melinda Gates Foundation</funding_body>
                <code>INV-002916</code>
            </grant_reference>
        </grant_support>
        <title>GT1.1 SOSIP-CC2 in complex with wk80 polyclonal antibodies from NHP 8229 (V1V2V3, C3V5, CD4bs, gp41GH/FP and base epitopes)</title>
        <authors_list>
            <author ORCID="0000-0002-2020-2991">Sewell LM</author>
            <author ORCID="0000-0002-9695-8138">Ozorowski G</author>
            <author ORCID="0000-0001-7153-3769">Ward AB</author>
        </authors_list>
        <keywords>polyclonal antibodies, non-human primate, germline targeting, HIV, Env, vaccine design, EMPEM, infant macaque, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0003-4647-7667" order="1">Nelson AN</author>
                    <author ORCID="0000-0002-8387-3952" order="2">Shen X</author>
                    <author ORCID="0000-0001-8976-6827" order="3">Vekatayogi S</author>
                    <author ORCID="0000-0003-4586-0605" order="4">Zhang S</author>
                    <author ORCID="0000-0002-9695-8138" order="5">Ozorowski G</author>
                    <author ORCID="0000-0003-0833-2635" order="6">Dennis M</author>
                    <author ORCID="0000-0002-2020-2991" order="7">Sewall LM</author>
                    <author ORCID="0000-0001-5062-6253" order="8">Milligan E</author>
                    <author order="9">Davis D</author>
                    <author ORCID="0000-0002-6455-9220" order="10">Cross KA</author>
                    <author ORCID="0000-0002-4977-8724" order="11">Chen Y</author>
                    <author ORCID="0000-0002-5202-355X" order="12">van Schooten J</author>
                    <author ORCID="0000-0002-1731-9806" order="13">Eudailey J</author>
                    <author ORCID="0000-0003-1133-7955" order="14">Isaac J</author>
                    <author ORCID="0009-0002-2460-0679" order="15">Memon S</author>
                    <author ORCID="0009-0006-8009-8010" order="16">Weinbaum C</author>
                    <author ORCID="0000-0002-2468-8589" order="17">Gao H</author>
                    <author ORCID="0000-0002-6347-1956" order="18">Stanfield-Oakley S</author>
                    <author order="19">Byrd A</author>
                    <author order="20">Chutkan S</author>
                    <author ORCID="0000-0001-9622-2238" order="21">Berendam S</author>
                    <author ORCID="0000-0002-5984-5978" order="22">Cronin K</author>
                    <author ORCID="0000-0002-2386-8991" order="23">Yasmeen A</author>
                    <author ORCID="0000-0003-0941-0703" order="24">Alam S</author>
                    <author ORCID="0000-0002-6653-6655" order="25">LaBranche CC</author>
                    <author ORCID="0000-0002-3911-035X" order="26">Rogers K</author>
                    <author ORCID="0000-0002-8403-451X" order="27">Shirreff L</author>
                    <author ORCID="0000-0001-7579-3525" order="28">Cupo A</author>
                    <author order="29">Derking R</author>
                    <author ORCID="0000-0002-7790-2008" order="30">Villinger F</author>
                    <author ORCID="0000-0001-8222-278X" order="31">Klasse PJ</author>
                    <author ORCID="0000-0001-7747-3349" order="32">Ferrari G</author>
                    <author ORCID="0000-0002-2970-7259" order="33">Williams WB</author>
                    <author ORCID="0000-0002-9106-4194" order="34">Hudgens MG</author>
                    <author ORCID="0000-0001-7153-3769" order="35">Ward AB</author>
                    <author ORCID="0000-0003-0856-6319" order="36">Montefiori DC</author>
                    <author ORCID="0000-0002-7375-1337" order="37">Van Rompay KKA</author>
                    <author ORCID="0000-0001-9933-9618" order="38">Wiehe K</author>
                    <author ORCID="0000-0002-9902-6096" order="39">Moore JP</author>
                    <author ORCID="0000-0002-2324-8573" order="40">Sanders RW</author>
                    <author ORCID="0000-0001-5199-3004" order="41">De Paris K</author>
                    <author ORCID="0000-0003-1438-4554" order="42">Permar SR</author>
                    <title>Immunization with germ line-targeting SOSIP trimers elicits broadly neutralizing antibody precursors in infant macaques.</title>
                    <journal_abbreviation>Sci Immunol</journal_abbreviation>
                    <country>US</country>
                    <volume>9</volume>
                    <first_page>eadm7097</first_page>
                    <last_page>eadm7097</last_page>
                    <year>2024</year>
                    <external_references type="PUBMED">39213340</external_references>
                    <external_references type="DOI">doi:10.1126/sciimmunol.adm7097</external_references>
                    <external_references type="ISSN">2470-9468</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>GT1.1 SOSIP-CC2 in complex with wk80 polyclonal antibodies from NHP 8229 (V1V2V3, C3V5, CD4bs, gp41GH/FP and base epitopes)</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>GT1.1 SOSIP-CC2 in complex with wk80 polyclonal antibodies from NHP 8229 (V1V2V3, C3V5, CD4bs, gp41GH/FP and base epitopes)</name>
                <parent>0</parent>
                <details>non-human primate polyclonal antibody Fab</details>
                <natural_source database="NCBI">
                    <organism ncbi="9544">Macaca mulatta</organism>
                </natural_source>
            </complex_supramolecule>
            <complex_supramolecule supramolecule_id="2">
                <name>GT1.1 SOSIP-CC2 in complex with wk80 polyclonal antibodies from NHP 8229 (V1V2V3, C3V5, CD4bs, gp41GH/FP and base epitopes)</name>
                <parent>1</parent>
                <details>GT1.1 SOSIP trimer</details>
                <natural_source database="NCBI">
                    <organism ncbi="11676">Human immunodeficiency virus 1</organism>
                </natural_source>
            </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">0.03</concentration>
                    <buffer>
                        <ph>7.4</ph>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <material>uranyl formate</material>
                        <details>2% w/v</details>
                    </staining>
                </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>
                    <nominal_defocus_min units="µm">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">1.5</nominal_defocus_max>
                    <nominal_magnification>62000.0</nominal_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>TVIPS TEMCAM-F416 (4k x 4k)</film_or_detector_model>
                            <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>
                <startup_model type_of_model="EMDB MAP">
                    <emdb_id>EMD-20396</emdb_id>
                    <details>low pass filtered to 40 Angstrom</details>
                </startup_model>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">25.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                    <number_images_used>8319</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="28312">
        <file>emd_41977.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>192</col>
            <row>192</row>
            <sec>192</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>192</x>
            <y>192</y>
            <z>192</z>
        </spacing>
        <cell>
            <a units="Å">339.84</a>
            <b units="Å">339.84</b>
            <c units="Å">339.84</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>-0.02785225</minimum>
            <maximum>0.05230482</maximum>
            <average>0.0006325427</average>
            <std>0.004782707</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.77</x>
            <y units="Å">1.77</y>
            <z units="Å">1.77</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0067</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-41977::::</label>
        <annotation_details>main map</annotation_details>
    </map>
    <interpretation>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="28312">
                <file>emd_41977_half_map_1.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>192</col>
                    <row>192</row>
                    <sec>192</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>192</x>
                    <y>192</y>
                    <z>192</z>
                </spacing>
                <cell>
                    <a units="Å">339.84</a>
                    <b units="Å">339.84</b>
                    <c units="Å">339.84</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>-0.034946974</minimum>
                    <maximum>0.061276745</maximum>
                    <average>0.0006284914</average>
                    <std>0.005211812</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.77</x>
                    <y units="Å">1.77</y>
                    <z units="Å">1.77</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-41977::::</label>
                <annotation_details>half map 1</annotation_details>
            </half_map>
            <half_map format="CCP4" size_kbytes="28312">
                <file>emd_41977_half_map_2.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>192</col>
                    <row>192</row>
                    <sec>192</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>192</x>
                    <y>192</y>
                    <z>192</z>
                </spacing>
                <cell>
                    <a units="Å">339.84</a>
                    <b units="Å">339.84</b>
                    <c units="Å">339.84</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>-0.037653606</minimum>
                    <maximum>0.061773855</maximum>
                    <average>0.0006477152</average>
                    <std>0.0052221357</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.77</x>
                    <y units="Å">1.77</y>
                    <z units="Å">1.77</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-41977::::</label>
                <annotation_details>half map 2</annotation_details>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
