<?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_11_0/emdb.xsd" version="3.0.11.0" emdb_id="EMD-46047">
    <admin>
        <current_status>
            <date>2025-06-25</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2024-08-02</deposition>
            <header_release>2025-05-28</header_release>
            <map_release>2025-05-28</map_release>
            <update>2025-06-25</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)</funding_body>
                <code>P01 AI157299</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>HIV Env JRFL NFL TD CC3+ trimer in complex with NHP #1 polyclonal Fab (gp120 interface, gp41-FP, gp41-base epitopes)</title>
        <authors_list>
            <author ORCID="0000-0002-2020-2991">Sewall LM</author>
            <author ORCID="0000-0002-9695-8138">Ozorowski G</author>
            <author ORCID="0000-0001-7153-3769">Ward AB</author>
        </authors_list>
        <keywords>NHP, rhesus macaque, gp120 interface, polyclonal, HIV, NFL, EMPEM, VIRAL PROTEIN-IMMUNE SYSTEM complex, VIRAL PROTEIN</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Schleich FA</author>
                    <author order="2">Bale S</author>
                    <author order="3">Guenaga J</author>
                    <author order="4">Ozorowski G</author>
                    <author order="5">Adori M</author>
                    <author order="6">Lin X</author>
                    <author order="7">Castro Dopico X</author>
                    <author order="8">Wilson R</author>
                    <author order="9">Chernyshev M</author>
                    <author order="10">Cotgreave AT</author>
                    <author order="11">Mandolesi M</author>
                    <author order="12">Cluff J</author>
                    <author order="13">Doyle ED</author>
                    <author order="14">Sewall LM</author>
                    <author order="15">Lee WH</author>
                    <author order="16">Zhang S</author>
                    <author order="17">O'Dell S</author>
                    <author order="18">Healy BS</author>
                    <author order="19">Lim D</author>
                    <author order="20">Lewis VR</author>
                    <author order="21">Ben-Akiva E</author>
                    <author order="22">Irvine DJ</author>
                    <author order="23">Doria-Rose NA</author>
                    <author order="24">Corcoran M</author>
                    <author order="25">Carnathan D</author>
                    <author order="26">Silvestri G</author>
                    <author order="27">Wilson IA</author>
                    <author order="28">Ward AB</author>
                    <author order="29">Karlsson Hedestam GB</author>
                    <author order="30">Wyatt RT</author>
                    <title>Vaccination of nonhuman primates elicits a broadly neutralizing antibody lineage targeting a quaternary epitope on the HIV-1 Env trimer.</title>
                    <journal_abbreviation>Immunity</journal_abbreviation>
                    <country>US</country>
                    <volume>58</volume>
                    <first_page>1598</first_page>
                    <last_page>1613.e8</last_page>
                    <year>2025</year>
                    <external_references type="PUBMED">40339576</external_references>
                    <external_references type="DOI">doi:10.1016/j.immuni.2025.04.010</external_references>
                    <external_references type="ISSN">1074-7613</external_references>
                    <external_references type="CSD">2048</external_references>
                    <external_references type="ASTM">IUNIEH</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>HIV Env JRFL NFL TD CC3+ trimer in complex with NHP #1 polyclonal Fab (gp120 interface, gp41-FP, gp41-base epitopes)</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>HIV Env JRFL NFL TD CC3+ trimer in complex with NHP #1 polyclonal Fab (gp120 interface, gp41-FP, gp41-base epitopes)</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="9544">Macaca mulatta</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">0.02</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <details>Tris-buffered saline</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <material>uranyl formate</material>
                    </staining>
                    <grid>
                        <model>Homemade</model>
                        <material>COPPER</material>
                        <mesh>400</mesh>
                        <support_film film_type_id="1">
                            <film_material>PARLODION</film_material>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                        </pretreatment>
                    </grid>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI SPIRIT</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <nominal_defocus_min units="µm">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">1.5</nominal_defocus_max>
                    <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/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>
                <ctf_correction>
                    <type>NONE</type>
                </ctf_correction>
                <startup_model type_of_model="PDB ENTRY">
                    <pdb_model>
                        <pdb_id>4ZMJ</pdb_id>
                    </pdb_model>
                    <details>coordinates converted to map using Chimera molmap</details>
                </startup_model>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">28.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                    <number_images_used>3088</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_46047.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">395.52</a>
            <b units="Å">395.52</b>
            <c units="Å">395.52</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>-0.035922766</minimum>
            <maximum>0.09044231</maximum>
            <average>0.00008635218</average>
            <std>0.004495426</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">2.06</x>
            <y units="Å">2.06</y>
            <z units="Å">2.06</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.02</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-46047::::</label>
        <annotation_details>main map</annotation_details>
    </map>
    <interpretation>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="28312">
                <file>emd_46047_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">395.52</a>
                    <b units="Å">395.52</b>
                    <c units="Å">395.52</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>-0.048249893</minimum>
                    <maximum>0.105872124</maximum>
                    <average>0.00008820345</average>
                    <std>0.0054972395</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">2.06</x>
                    <y units="Å">2.06</y>
                    <z units="Å">2.06</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-46047::::</label>
                <annotation_details>half map B</annotation_details>
            </half_map>
            <half_map format="CCP4" size_kbytes="28312">
                <file>emd_46047_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">395.52</a>
                    <b units="Å">395.52</b>
                    <c units="Å">395.52</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>-0.04881635</minimum>
                    <maximum>0.1045312</maximum>
                    <average>0.000065963046</average>
                    <std>0.00547682</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">2.06</x>
                    <y units="Å">2.06</y>
                    <z units="Å">2.06</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-46047::::</label>
                <annotation_details>half map A</annotation_details>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
