<emd emdb_id="EMD-6238" 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>2015-01-06</deposition>
            <header_release>2015-03-18</header_release>
            <map_release>2015-07-22</map_release>
            <update>2015-07-22</update>
        </key_dates>
        <title>Negative stain single particle electron microscopy of Marburg Virus Glycoproteins bound to antibodies from a human survivor</title>
        <authors_list>
            <author>Flyak A</author>
            <author>Ilinykh PA</author>
            <author>Murin CD</author>
            <author>Garron T</author>
            <author>Shen X</author>
            <author>Fusco ML</author>
            <author>Hashiguchi T</author>
            <author>Bornholdt ZA</author>
            <author>Slaughter C</author>
            <author>Sapparapu G</author>
            <author>Ksiazek TG</author>
            <author>Ward AB</author>
            <author>Saphire EO</author>
            <author>Bukreyev A</author>
            <author>Crowe JE</author>
        </authors_list>
        <keywords>Marburg Virus, Antibodies, Neutralization, Glycoprotein</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Flyak AI</author>
                    <author order="2">Ilinykh PA</author>
                    <author order="3">Murin CD</author>
                    <author order="4">Garron T</author>
                    <author order="5">Shen X</author>
                    <author order="6">Fusco ML</author>
                    <author order="7">Hashiguchi T</author>
                    <author order="8">Bornholdt ZA</author>
                    <author order="9">Slaughter JC</author>
                    <author order="10">Sapparapu G</author>
                    <author order="11">Ksiazek TG</author>
                    <author order="12">Ward AB</author>
                    <author order="13">Saphire EO</author>
                    <author order="14">Bukreyev A</author>
                    <author order="15">Crowe Jr JE</author>
                    <title>Mechanism of human antibody-mediated neutralization of Marburg virus</title>
                    <journal>CELL(CAMBRIDGE,MASS.)</journal>
                    <volume>160</volume>
                    <first_page>893</first_page>
                    <last_page>903</last_page>
                    <year>2015</year>
                    <external_references type="PUBMED">25723164</external_references>
                    <external_references type="DOI">doi:10.1016/j.cell.2015.01.031</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Fab Fragment of MR198 human IgG1 monoclonal antibody to Marburg Virus GP</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Fab Fragment of MR198 human IgG1 monoclonal antibody to Marburg Virus GP</name>
                <oligomeric_state>trimer</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="glycoprotein">GP, mucin-deleted</name>
                <natural_source database="NCBI">
                    <organism>Marburg marburgvirus</organism>
                    <synonym_organism>Marburg virus</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">160</theoretical>
                </molecular_weight>
                <details>Recombinant Marburg Virus GP; mucin-like domains were not included in the construct.</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 S2 cells</recombinant_cell>
                    <recombinant_plasmid>pMT-puro</recombinant_plasmid>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name synonym="IgG1, monoclonal mAb">Human Monoclonal Antibody IgG1</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                    <tissue>Blood</tissue>
                    <cell>Peripheral blood mononuclear cells</cell>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.15</theoretical>
                </molecular_weight>
                <details>Human monoclonal antibody IgG1, MR198</details>
                <number_of_copies>1</number_of_copies>
                <oligomeric_state>monomer</oligomeric_state>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <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>Grids with absorbed protein stained with 2% uranyl formate for 30 seconds</details>
                    </staining>
                    <grid>
                        <details>400 mesh copper grid with carbon support, plasma cleaned 20 seconds (Ar/O2 mix, Gatan)</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 SPIRIT</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>2013-11-12</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">OTHER</film_or_detector_model>
                            <number_real_images>167</number_real_images>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Particles were selected using DoG picker.</details>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <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>4974</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="2001">
        <file>emd_6238.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>-8.441008569999999</minimum>
            <maximum>13.269314769999999</maximum>
            <average>0.0</average>
            <std>0.99999905</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>4.9</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of Marburg Virus GPdMuc bound to antibody MR198 from a human survivor</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6238::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_6238.jpg</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>