<emd emdb_id="EMD-6356" 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>2015-06-16</deposition>
            <header_release>2015-08-19</header_release>
            <map_release>2015-11-18</map_release>
            <update>2016-06-22</update>
        </key_dates>
        <title>Electron cryo-microscopy of Chikungunya virus-like particles in complex with neutralizing antibody Fab 5F10</title>
        <authors_list>
            <author>Porta JC</author>
            <author>Mangala Prasad V</author>
            <author>Akahata W</author>
            <author>Wang CI</author>
            <author>Ng L</author>
            <author>Rossmann MG</author>
        </authors_list>
        <keywords>Virus-like particle, Chikungunya, Fab, Antibody</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Porta J</author>
                    <author order="2">Prasad VM</author>
                    <author order="3">Wang CI</author>
                    <author order="4">Akahata W</author>
                    <author order="5">Ng LF</author>
                    <author order="6">Rossmann MG</author>
                    <title>Structural Studies of Chikungunya Virus-like Particles Complexed with Human Antibodies: Neutralization and Cell-to-Cell Transmission.</title>
                    <journal>J.VIROL.</journal>
                    <volume>90</volume>
                    <first_page>1169</first_page>
                    <last_page>1177</last_page>
                    <year>2016</year>
                    <external_references type="PUBMED">26537684</external_references>
                    <external_references type="DOI">doi:10.1128/JVI.02364-15</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Fab fragment of monoclonal antibody 5F10 bound to Chikungunya virus-like particles</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Fab fragment of monoclonal antibody 5F10 bound to Chikungunya virus-like particles</name>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">5.25</experimental>
                </molecular_weight>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="CHIK-VLP">Chikungunya virus</name>
                <sci_species_name ncbi="37124">Chikungunya virus</sci_species_name>
                <sci_species_strain>LR2006 OPY-1</sci_species_strain>
                <natural_host database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>VERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI">
                    <recombinant_organism ncbi="10026">Cricetinae</recombinant_organism>
                    <recombinant_cell>BHK-15</recombinant_cell>
                    <recombinant_plasmid>E37997, Eopy-1</recombinant_plasmid>
                </host_system>
                <molecular_weight>
                    <experimental units="MDa">5.25</experimental>
                </molecular_weight>
                <virus_shell shell_id="1">
                    <name>E1E2</name>
                    <diameter units="&#8491;">700</diameter>
                    <triangulation>4</triangulation>
                </virus_shell>
                <virus_type>VIRUS-LIKE PARTICLE</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>true</virus_enveloped>
                <virus_empty>true</virus_empty>
                <syn_species_name>CHIK-VLP</syn_species_name>
            </virus_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>neutralizing antibody Fab 5F10</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>human</synonym_organism>
                </natural_source>
                <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">2</concentration>
                    <buffer>
                        <ph>7.6</ph>
                        <details>PBS</details>
                    </buffer>
                    <grid>
                        <details>400 mesh Cu holey carbon</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <chamber_temperature units="K">93</chamber_temperature>
                        <instrument>GATAN CRYOPLUNGE 3</instrument>
                        <method>Blot for 5 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>FLOOD BEAM</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</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.185</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">0.35</nominal_defocus_max>
                    <nominal_magnification>59000.0</nominal_magnification>
                    <calibrated_magnification>60521.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">80</temperature_min>
                        <temperature_max units="K">100</temperature_max>
                        <temperature_average units="K">95</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 96,000 times magnification.</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2014-06-03</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">FEI CETA (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">2.5</sampling_interval>
                            </digitization_details>
                            <number_real_images>102</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">22</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Nitrogen-cooled</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>Each image</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">18.1</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN</name>
                        </software>
                    </software_list>
                    <number_images_used>1621</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>10</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="182251">
        <file>emd_6356.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>360</col>
            <row>360</row>
            <sec>360</sec>
        </dimensions>
        <origin>
            <col>-179</col>
            <row>-179</row>
            <sec>-179</sec>
        </origin>
        <spacing>
            <x>360</x>
            <y>360</y>
            <z>360</z>
        </spacing>
        <cell>
            <a units="&#8491;">1080.0</a>
            <b units="&#8491;">1080.0</b>
            <c units="&#8491;">1080.0</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>-3.89509726</minimum>
            <maximum>3.27364659</maximum>
            <average>0.00009319</average>
            <std>0.40813154</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">3.0</x>
            <y units="&#8491;">3.0</y>
            <z units="&#8491;">3.0</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.5</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>CHIK-VLP complexed to Fab 5F10</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6356::::</details>
    </map>
</emd>