<emd emdb_id="EMD-5578" 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>2013-01-28</deposition>
            <header_release>2013-03-20</header_release>
            <map_release>2013-04-24</map_release>
            <update>2013-04-24</update>
        </key_dates>
        <title>Electron Cryo-microscopy of Chikungunya VLP in complex with neutralizing antibody Fab 9.8B</title>
        <authors_list>
            <author>Sun S</author>
            <author>Xiang Y</author>
            <author>Rossmann MG</author>
        </authors_list>
        <keywords>Alpha virus, Chikungunya VLP, neutralizing antibody 9.8B</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Sun S</author>
                    <author order="2">Xiang Y</author>
                    <author order="3">Akahata W</author>
                    <author order="4">Holdaway H</author>
                    <author order="5">Pal P</author>
                    <author order="6">Zhang X</author>
                    <author order="7">Diamond MS</author>
                    <author order="8">Nabel GJ</author>
                    <author order="9">Rossmann MG</author>
                    <title>Structural analyses at pseudo atomic resolution of Chikungunya virus and antibodies show mechanisms of neutralization.</title>
                    <journal>ELIFE</journal>
                    <volume>2</volume>
                    <first_page>e00435</first_page>
                    <last_page>e00435</last_page>
                    <year>2013</year>
                    <external_references type="PUBMED">23577234</external_references>
                    <external_references type="DOI">doi:10.7554/eLife.00435</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3j2y</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Electron Cryo-microscopy of Chikungunya VLP in complex with neutralizing antibody Fab 9.8B</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Electron Cryo-microscopy of Chikungunya VLP in complex with neutralizing antibody Fab 9.8B</name>
                <number_unique_components>2</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name>Chikungunya virus</name>
                <sci_species_name ncbi="37124">Chikungunya virus</sci_species_name>
                <sci_species_strain>37997</sci_species_strain>
                <natural_host database="NCBI">
                    <organism ncbi="7160">Aedes albopictus</organism>
                    <synonym_organism>INVERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI">
                    <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
                    <recombinant_cell>HEK 293T</recombinant_cell>
                    <recombinant_plasmid>CMV/R</recombinant_plasmid>
                </host_system>
                <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>false</virus_empty>
            </virus_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>9.8B antibody Fab fragment</name>
                <natural_source database="NCBI">
                    <organism ncbi="10090">Mus musculus</organism>
                    <synonym_organism>mouse</synonym_organism>
                    <cell>Hybridoma</cell>
                </natural_source>
                <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">1</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <details>PBS</details>
                    </buffer>
                    <grid>
                        <details>400 mesh C-flat grids</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">95</chamber_humidity>
                        <chamber_temperature units="K">90</chamber_temperature>
                        <instrument>GATAN CRYOPLUNGE 3</instrument>
                        <method>Blot for 2 seconds before plunging.</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI/PHILIPS CM300FEG/HE</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_magnification>38000.0</nominal_magnification>
                    <calibrated_magnification>39190.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 100,000 times magnification</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2011-02-01</date>
                    <image_recording_list>
                        <image_recording>
                            <digitization_details>
                                <scanner>NIKON SUPER COOLSCAN 9000</scanner>
                                <sampling_interval units="&#181;m">6.35</sampling_interval>
                            </digitization_details>
                            <number_real_images>100</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Side entry liquid nitrogen-cooled cryo specimen holder</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>The particles were selected using e2boxer.</details>
                <ctf_correction>
                    <details>each micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">14.9</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN2</name>
                        </software>
                    </software_list>
                    <number_images_used>1820</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="250001">
        <file>emd_5578.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>400</col>
            <row>400</row>
            <sec>400</sec>
        </dimensions>
        <origin>
            <col>-200</col>
            <row>-200</row>
            <sec>-200</sec>
        </origin>
        <spacing>
            <x>400</x>
            <y>400</y>
            <z>400</z>
        </spacing>
        <cell>
            <a units="&#8491;">888.0</a>
            <b units="&#8491;">888.0</b>
            <c units="&#8491;">888.0</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>-2.45126295</minimum>
            <maximum>8.965277670000001</maximum>
            <average>0.5157069</average>
            <std>1.25874364</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.22</x>
            <y units="&#8491;">2.22</y>
            <z units="&#8491;">2.22</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of Chikungunya VLP with neutralizing antibody 9.8B</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5578::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>4GQ9</access_code>
                    <chain>
                        <chain_id>A</chain_id>
                    </chain>
                    <chain>
                        <chain_id>B</chain_id>
                    </chain>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>EMfit</name>
                    </software>
                </software_list>
                <target_criteria>Sumf</target_criteria>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
        <figure_list>
            <figure>
                <file>emd_5578.png</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>