<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-6257" version="3.0.1.9">
    <admin>
        <status_history_list>
            <status status_id="1">
                <code>HPUB</code>
            </status>
        </status_history_list>
        <current_status>
            <code>OBS</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2015-01-24</deposition>
            <header_release>2015-03-18</header_release>
            <obsolete>2016-07-20</obsolete>
            <update>2016-07-20</update>
        </key_dates>
        <title>Cryo-EM structure of Dengue virus serotype 1 complexed with Fab fragments of human antibody D11C</title>
        <authors_list>
            <author>Dip PV</author>
            <author>Fibriansah G</author>
            <author>Ng TS</author>
            <author>Wang J</author>
            <author>Kukkaro P</author>
            <author>Kostyuchenko VA</author>
            <author>Robinson JE</author>
            <author>Isern S</author>
            <author>Michael SF</author>
            <author>Anand G</author>
            <author>Schieffelin JS</author>
            <author>Lok SM</author>
        </authors_list>
        <keywords>antibody, Dengue virus, fusion loop</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Dip PV</author>
                    <author order="2">Fibriansah G</author>
                    <author order="3">Ng TS</author>
                    <author order="4">Wang J</author>
                    <author order="5">Kukkaro P</author>
                    <author order="6">Kostyuchenko VA</author>
                    <author order="7">Robinson JE</author>
                    <author order="8">Isern S</author>
                    <author order="9">Michael SF</author>
                    <author order="10">Anand G</author>
                    <author order="11">Schieffelin JS</author>
                    <author order="12">Lok SM</author>
                    <title>Antibody-Dengue virus complex shows neutralization mechanism by the pre-dominant human antibodies</title>
                    <journal>To Be Published</journal>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3j9h</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Dengue virus serotype 1 with variable domain of Fab fragments of human monoclonal antibody D11C</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Dengue virus serotype 1 with variable domain of Fab fragments of human monoclonal antibody D11C</name>
                <oligomeric_state>60 Fab molecules bind to one Dengue virion</oligomeric_state>
                <number_unique_components>2</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name>Dengue virus 1</name>
                <sci_species_name ncbi="11053">Dengue virus 1</sci_species_name>
                <sci_species_strain>PVP159</sci_species_strain>
                <natural_host database="NCBI">
                    <organism ncbi="7159">Aedes aegypti</organism>
                    <synonym_organism>INVERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI">
                    <recombinant_organism ncbi="7160">Aedes albopictus</recombinant_organism>
                    <recombinant_cell>C6/36 cells</recombinant_cell>
                </host_system>
                <virus_type>VIRION</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>true</virus_enveloped>
                <virus_empty>false</virus_empty>
            </virus_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>antibody D11C Fab, variable region</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>human</synonym_organism>
                </natural_source>
                <number_of_copies>60</number_of_copies>
                <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">
                    <buffer>
                        <ph>8.0</ph>
                        <details>12 mM Tris-HCl, pH 8.0, 120 mM NaCl, 1 mM EDTA</details>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">100</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>Blot with filter paper for 2 seconds before plunging.</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</microscope>
                    <illumination_mode>SPOT SCAN</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">4.0</nominal_defocus_max>
                    <nominal_magnification>47000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">100</temperature_average>
                    </temperature>
                    <specialist_optics>
                        <energy_filter>
                            <name>FEI</name>
                        </energy_filter>
                    </specialist_optics>
                    <date>2013-08-10</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">FEI FALCON I (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">18.1</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>The particles were selected manually.</details>
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">21.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN2, RELION, MPSA</name>
                        </software>
                    </software_list>
                    <number_images_used>8537</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>100</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
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        <file>emd_6257.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>512</col>
            <row>512</row>
            <sec>512</sec>
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        <origin>
            <col>-256</col>
            <row>-256</row>
            <sec>-256</sec>
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        <spacing>
            <x>512</x>
            <y>512</y>
            <z>512</z>
        </spacing>
        <cell>
            <a units="Å">875.52</a>
            <b units="Å">875.52</b>
            <c units="Å">875.52</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>
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        <statistics>
            <minimum>-10.19386959</minimum>
            <maximum>16.27508354</maximum>
            <average>-0.13167311</average>
            <std>1.00621843</std>
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        <pixel_spacing>
            <x units="Å">1.71</x>
            <y units="Å">1.71</y>
            <z units="Å">1.71</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.5</level>
                <source>AUTHOR</source>
            </contour>
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        <annotation_details>Cryo-EM structure of Dengue virus serotype 1 complexed with variable region of Fab fragments of human antibody D11C</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6257::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>1OAN</access_code>
                </initial_model>
                <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>O, Chimera, MDFF</name>
                    </software>
                </software_list>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
