<?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-21256">
    <admin>
        <current_status>
            <date>2024-10-16</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2020-01-29</deposition>
            <header_release>2020-07-01</header_release>
            <map_release>2020-07-01</map_release>
            <update>2024-10-16</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>UM1 AI100663</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)</funding_body>
                <code>UM1 AI144462</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)</funding_body>
                <code>F31 AI131873</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>BG505 SOSIP.v5.2 in complex with rabbit Fab 43A2</title>
        <authors_list>
            <author>Nogal B</author>
            <author>Cottrell CA</author>
        </authors_list>
        <keywords>HIV, Env, antibody, VIRAL PROTEIN</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0001-8977-7470" order="1">Nogal B</author>
                    <author ORCID="0000-0001-9503-7946" order="2">McCoy LE</author>
                    <author ORCID="0000-0003-3422-8161" order="3">van Gils MJ</author>
                    <author ORCID="0000-0002-3364-3083" order="4">Cottrell CA</author>
                    <author ORCID="0000-0002-4777-1596" order="5">Voss JE</author>
                    <author order="6">Andrabi R</author>
                    <author ORCID="0000-0001-9212-4307" order="7">Pauthner M</author>
                    <author order="8">Liang CH</author>
                    <author order="9">Messmer T</author>
                    <author order="10">Nedellec R</author>
                    <author ORCID="0000-0002-1607-5301" order="11">Shin M</author>
                    <author order="12">Turner HL</author>
                    <author ORCID="0000-0002-9695-8138" order="13">Ozorowski G</author>
                    <author order="14">Sanders RW</author>
                    <author ORCID="0000-0001-6711-9864" order="15">Burton DR</author>
                    <author ORCID="0000-0002-9778-1776" order="16">Ward AB</author>
                    <title>HIV envelope trimer-elicited autologous neutralizing antibodies bind a region overlapping the N332 glycan supersite.</title>
                    <journal_abbreviation>Sci Adv</journal_abbreviation>
                    <country>US</country>
                    <volume>6</volume>
                    <first_page>eaba0512</first_page>
                    <last_page>eaba0512</last_page>
                    <year>2020</year>
                    <external_references type="PUBMED">32548265</external_references>
                    <external_references type="DOI">doi:10.1126/sciadv.aba0512</external_references>
                    <external_references type="ISSN">2375-2548</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6vo0</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>BG505 SOSIP.v5.2 in complex with rabbit Fab 43A2</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>BG505 SOSIP.v5.2 in complex with rabbit Fab 43A2</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>3</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>4</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
            </complex_supramolecule>
            <complex_supramolecule supramolecule_id="2">
                <name>Fab 43A2</name>
                <parent>1</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="9986">Oryctolagus cuniculus</organism>
                </natural_source>
            </complex_supramolecule>
            <complex_supramolecule supramolecule_id="3">
                <name>BG505 SOSIP.v5.2</name>
                <parent>1</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>3</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>4</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="11676">Human immunodeficiency virus 1</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>43A2 light chain</name>
                <natural_source database="NCBI">
                    <organism ncbi="9986">Oryctolagus cuniculus</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.012078307</theoretical>
                </molecular_weight>
                <number_of_copies>3</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>DIVMTQTPASVSEPVGGTVTIKCQASHNIRSYLSWYQQKVGQPPKRLIYETSNLASGVPSRFAGSGSGTEFTLTISDLEC
ADAATYYCQSNFGLSDSRTYNFGGGTEVVVKGD</string>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>43A2 heavy chain</name>
                <natural_source database="NCBI">
                    <organism ncbi="9986">Oryctolagus cuniculus</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.013025552999999999</theoretical>
                </molecular_weight>
                <number_of_copies>3</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>RQLVESGGGLVQPEGSLTLTCKASGFSFSRSQYMCWVRQAPGKGLEWITCVYPDDDTPYYATWAKGRFTISKTSSTTVTL
RLTSLTEADTATYFCARTSGFGGYSYAAHGVDLWGPGTLV</string>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name>Envelope glycoprotein gp120</name>
                <natural_source database="NCBI">
                    <organism ncbi="11676">Human immunodeficiency virus 1</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.053268370999999995</theoretical>
                </molecular_weight>
                <number_of_copies>3</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>AENLWVTVYYGVPVWKDAETTLFCASDAKAYETKKHNVWATHCCVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIIS
LWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKE
YRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQWFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRK
HFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQ
AMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVG</string>
                    <external_references type="UNIPROTKB">Q2N0S6</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="4">
                <name>Envelope glycoprotein gp41</name>
                <natural_source database="NCBI">
                    <organism ncbi="11676">Human immunodeficiency virus 1</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.017178548999999998</theoretical>
                </molecular_weight>
                <number_of_copies>3</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPECQQHLLKLTVWGIKQLQARVLAVERYLRDQQ
LLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD</string>
                    <external_references type="UNIPROTKB">Q2N0S6</external_references>
                </sequence>
            </protein_or_peptide>
            <ligand macromolecule_id="7">
                <name>2-acetamido-2-deoxy-beta-D-glucopyranose</name>
                <molecular_weight>
                    <theoretical units="MDa">0.000221208</theoretical>
                </molecular_weight>
                <number_of_copies>27</number_of_copies>
                <formula>NAG</formula>
            </ligand>
        </macromolecule_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>7.4</ph>
                    </buffer>
                    <grid>
                        <details>unspecified</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_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>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <average_electron_dose_per_image units="e/Å^2">49.6</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="OTHER"/>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C3</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">3.52</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>1</version>
                        </software>
                    </software_list>
                    <number_images_used>85841</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="105855">
        <file>emd_21256.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>298</col>
            <row>298</row>
            <sec>298</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>298</x>
            <y>298</y>
            <z>298</z>
        </spacing>
        <cell>
            <a units="Å">306.94</a>
            <b units="Å">306.94</b>
            <c units="Å">306.94</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>-1.0131671</minimum>
            <maximum>2.3790114</maximum>
            <average>0.0024776072</average>
            <std>0.0821924</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.03</x>
            <y units="Å">1.03</y>
            <z units="Å">1.03</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.5</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-21256::::</label>
        <annotation_details>BG505 SOSIP.v5.2 in complex with rabbit Fab 43A2</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
