<emd emdb_id="EMD-6150" 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>2014-10-25</deposition>
            <header_release>2014-11-19</header_release>
            <map_release>2014-11-19</map_release>
            <update>2014-12-10</update>
        </key_dates>
        <title>Structures of Protective Antibodies Reveal Sites of Vulnerability on Ebola Virus</title>
        <authors_list>
            <author>Murin CD</author>
            <author>Fusco ML</author>
            <author>Bornholdt ZA</author>
            <author>Qiu X</author>
            <author>Olinger GG</author>
            <author>Zeitlin L</author>
            <author>Kobinger GP</author>
            <author>Ward AB</author>
            <author>Saphire EO</author>
        </authors_list>
        <keywords>Ebola, Antibody cocktails, mAbs, ZMAb, ZMapp, MB-003</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Murin CD</author>
                    <author order="2">Fusco ML</author>
                    <author order="3">Bornholdt ZA</author>
                    <author order="4">Qiu X</author>
                    <author order="5">Olinger GG</author>
                    <author order="6">Zeitlin L</author>
                    <author order="7">Kobinger GP</author>
                    <author order="8">Ward AB</author>
                    <author order="9">Saphire EO</author>
                    <title>Structures of Protective Antibodies Reveal Sites of Vulnerability on Ebola Virus</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <volume>111</volume>
                    <first_page>17182</first_page>
                    <last_page>17187</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">25404321</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1414164111</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Complex of Ebola virus glycoprotein with transmembrane region and cytoplasmic tail removed (GPdTM) in complex with Fab fragments of c1H3 chimerized human IgG1 and human KZ52 IgG1 antibodies to Ebola virus GP</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Complex of Ebola virus glycoprotein with transmembrane region and cytoplasmic tail removed (GPdTM) in complex with Fab fragments of c1H3 chimerized human IgG1 and human KZ52 IgG1 antibodies to Ebola virus GP</name>
                <oligomeric_state>Ebola GP trimer bound to six Fab fragments (two per monomer)</oligomeric_state>
                <number_unique_components>3</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">0.75</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="EBOV GP">Ebola virus GP</name>
                <natural_source database="NCBI">
                    <organism ncbi="205488">Ebola virus sp.</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.45</theoretical>
                </molecular_weight>
                <details>transmembrane and cytoplasmic tail removed</details>
                <number_of_copies>1</number_of_copies>
                <oligomeric_state>trimer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="7227">Drosophila melanogaster</recombinant_organism>
                    <recombinant_cell>Schneider 2 (S2)</recombinant_cell>
                    <recombinant_plasmid>pMT-puro</recombinant_plasmid>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name synonym="c1H3 Fab">chimerized human IgG1 antigen binding fragment c1H3</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>human</synonym_organism>
                </natural_source>
                <number_of_copies>3</number_of_copies>
                <oligomeric_state>monomer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="4100">Nicotiana benthamiana</recombinant_organism>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name synonym="KZ52 Fab">chimerized human IgG1 antigen binding fragment KZ52</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>human</synonym_organism>
                </natural_source>
                <number_of_copies>3</number_of_copies>
                <oligomeric_state>monomer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="4100">Nicotiana benthamiana</recombinant_organism>
                </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>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>To prepare negative stain grids, a 4 uL aliquot of each complex, which had been diluted to a concentration of ~0.03 ug/mL with TBS buffer, was placed for 15 seconds onto carbon-coated 400 Cu mesh grids that had been plasma cleaned for 20 s (Gatan), blotted off on the edge of the grid, then immediately stained for 30 s with 4 uL of 2% uranyl formate. The stain was blotted off on the edge of the grid and the grid was allowed to dry.</details>
                    </staining>
                    <grid>
                        <details>400 Cu mesh grids, plasma-cleaned with Ag/O2 mix for 20 seconds</details>
                    </grid>
                    <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 F20</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>TUNGSTEN HAIRPIN</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <nominal_defocus_min units="&#181;m">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">1.0</nominal_defocus_max>
                    <nominal_magnification>52000.0</nominal_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <date>2014-01-15</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">OTHER</film_or_detector_model>
                            <number_real_images>23</number_real_images>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Particles selected and sorted using automatic selection program (DoG Picker, Xmipp) using Appion.</details>
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">24.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN2</name>
                        </software>
                    </software_list>
                    <number_images_used>2411</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="2001">
        <file>emd_6150.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>-4.40797615</minimum>
            <maximum>13.05906105</maximum>
            <average>0.00428074</average>
            <std>0.99983615</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>3.55</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of Ebola virus glycoprotein in complex with Fab fragments of c1H3 and KZ52</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6150::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_6150.jpg</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>