<emd emdb_id="EMD-6528" version="3.0.1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_1/emdb_relaxed.xsd">
    <admin>
        <current_status>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2015-11-20</deposition>
            <header_release>2016-04-06</header_release>
            <map_release>2016-04-06</map_release>
            <update>2016-04-06</update>
        </key_dates>
        <title>Negative stain EM reconstruction of Bundibugyo virus (BDBV) glycoprotein in complex with a human IgG1 Fab</title>
        <authors_list>
            <author>Flyak AI</author>
            <author>Shen X</author>
            <author>Murin CD</author>
            <author>Turner HL</author>
            <author>Fusco ML</author>
            <author>Lampley R</author>
            <author>Kose N</author>
            <author>Ilinykh PA</author>
            <author>Kuzmina N</author>
            <author>Branchizio A</author>
            <author>King H</author>
            <author>Brown L</author>
            <author>Davidson E</author>
            <author>Doranz BJ</author>
            <author>Slaughter JC</author>
            <author>Sapparapu G</author>
            <author>Klages C</author>
            <author>Ksiazek TG</author>
            <author>Saphire EO</author>
            <author>Ward AB</author>
            <author>Bukreyev A</author>
            <author>Crowe JE</author>
        </authors_list>
        <keywords>Ebola virus, EBOV, GP, antibody, Bundibugyo virus, BDBV, Fab</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Flyak AI</author>
                    <author order="2">Shen X</author>
                    <author order="3">Murin CD</author>
                    <author order="4">Turner HL</author>
                    <author order="5">David JA</author>
                    <author order="6">Fusco ML</author>
                    <author order="7">Lampley R</author>
                    <author order="8">Kose N</author>
                    <author order="9">Ilinykh PA</author>
                    <author order="10">Kuzmina N</author>
                    <author order="11">Branchizio A</author>
                    <author order="12">King H</author>
                    <author order="13">Brown L</author>
                    <author order="14">Bryan C</author>
                    <author order="15">Davidson E</author>
                    <author order="16">Doranz BJ</author>
                    <author order="17">Slaughter JC</author>
                    <author order="18">Sapparapu G</author>
                    <author order="19">Klages C</author>
                    <author order="20">Ksiazek TG</author>
                    <author order="21">Saphire EO</author>
                    <author order="22">Ward AB</author>
                    <author order="23">Bukreyev A</author>
                    <author order="24">Crowe JE</author>
                    <title>Cross-Reactive and Potent Neutralizing Antibody Responses in Human Survivors of Natural Ebolavirus Infection.</title>
                    <journal>CELL(CAMBRIDGE,MASS.)</journal>
                    <volume>164</volume>
                    <first_page>392</first_page>
                    <last_page>405</last_page>
                    <year>2016</year>
                    <external_references type="PUBMED">26806128</external_references>
                    <external_references type="DOI">doi:10.1016/j.cell.2015.12.022</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Fab fragment of BDBV41 human IgG1 monoclonal antibody to Bundibugyo virus in complex with mucin-deleted Bundibugyo virus GP</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Fab fragment of BDBV41 human IgG1 monoclonal antibody to Bundibugyo virus in complex with mucin-deleted Bundibugyo virus GP</name>
                <oligomeric_state>Three Fabs (each consisting of one heavy chain and one light chain) bind to a single GP (consisting of a trimer of heterodimers of GP1 and GP2)</oligomeric_state>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">0.31</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="Fab">human IgG1 monoclonal antibody Fab</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                    <cell>Peripheral blood mononuclear cells</cell>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.05</theoretical>
                </molecular_weight>
                <details>Fabs were generated by optimized papain proteolysis of IgG1. There are three Fabs bound to each trimeric GP.</details>
                <number_of_copies>3</number_of_copies>
                <oligomeric_state>heterodimer (one heavy chain, one light chain)</oligomeric_state>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name synonym="BDBV GP">Bundibugyo virus glycoprotein</name>
                <natural_source database="NCBI">
                    <organism ncbi="205488">Ebola virus sp.</organism>
                    <strain>Bundibugyo virus</strain>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.16</theoretical>
                </molecular_weight>
                <details>Recombinantly expressed ectodomain of Bundibugyo virus GP. Mucin-like domains were deleted from the expression construct, as were the transmembrane domains and cytoplasmic tail.</details>
                <number_of_copies>1</number_of_copies>
                <oligomeric_state>trimer of heterodimers (consisting of covalently linked GP1 and GP2)</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="7227">Drosophila melanogaster</recombinant_organism>
                    <recombinant_cell>S2</recombinant_cell>
                    <recombinant_plasmid>pMT puro</recombinant_plasmid>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
        </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">
                    <concentration units="mg/mL">0.03</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <details>20 mM Tris, 150 mM NaCl</details>
                    </buffer>
                    <vitrification>
                        <cryogen_name>NONE</cryogen_name>
                        <instrument>OTHER</instrument>
                    </vitrification>
                </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="&#181;m">1.0</nominal_defocus_min>
                    <calibrated_magnification>52000.0</calibrated_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <date>2015-03-05</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">TVIPS TEMCAM-F416 (4k x 4k)</film_or_detector_model>
                            <number_real_images>51</number_real_images>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">25.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Relion</name>
                        </software>
                    </software_list>
                    <number_images_used>919</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="2001">
        <file>emd_6528.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>80</col>
            <row>80</row>
            <sec>80</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>80</x>
            <y>80</y>
            <z>80</z>
        </spacing>
        <cell>
            <a units="&#8491;">328.0</a>
            <b units="&#8491;">328.0</b>
            <c units="&#8491;">328.0</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>-0.06337862</minimum>
            <maximum>0.11207981</maximum>
            <average>0.00051626</average>
            <std>0.00819055</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">4.1</x>
            <y units="&#8491;">4.1</y>
            <z units="&#8491;">4.1</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0377</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of Fab of human monoclonal antibody BDBV41 in complex with mucin-deleted Bundibugyo virus (BDBV) glycoprotein (GP)</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6528::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_6528.jpg</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>