<emd emdb_id="EMD-6466" 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>2015-09-13</deposition>
            <header_release>2015-10-14</header_release>
            <map_release>2016-01-13</map_release>
            <update>2016-01-13</update>
        </key_dates>
        <title>Cryo-EM of CHIKV VLP</title>
        <authors_list>
            <author>Jin J</author>
            <author>Liss N</author>
            <author>Chen D-H</author>
            <author>Liao M</author>
            <author>Fox JM</author>
            <author>Shimak RM</author>
            <author>Fong RH</author>
            <author>Chafets D</author>
            <author>Bakkour S</author>
            <author>Keating S</author>
            <author>Fomin ME</author>
            <author>Muench MO</author>
            <author>Sherman MB</author>
            <author>Doranz BJ</author>
            <author>Diamond MS</author>
            <author>Simmons G</author>
        </authors_list>
        <keywords>chikungunya, cryo-EM</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Jin J</author>
                    <author order="2">Liss NM</author>
                    <author order="3">Chen DH</author>
                    <author order="4">Liao M</author>
                    <author order="5">Fox JM</author>
                    <author order="6">Shimak RM</author>
                    <author order="7">Fong RH</author>
                    <author order="8">Chafets D</author>
                    <author order="9">Bakkour S</author>
                    <author order="10">Keating S</author>
                    <author order="11">Fomin ME</author>
                    <author order="12">Muench MO</author>
                    <author order="13">Sherman MB</author>
                    <author order="14">Doranz BJ</author>
                    <author order="15">Diamond MS</author>
                    <author order="16">Simmons G</author>
                    <title>Neutralizing Monoclonal Antibodies Block Chikungunya Virus Entry and Release by Targeting an Epitope Critical to Viral Pathogenesis</title>
                    <journal>Cell Rep.</journal>
                    <volume>13</volume>
                    <first_page>2553</first_page>
                    <last_page>2564</last_page>
                    <year>2015</year>
                    <external_references type="PUBMED">26686638</external_references>
                    <external_references type="DOI">doi:10.1016/j.celrep.2015.11.043</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Virus-like particle of Chikungunya virus (S27)</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Virus-like particle of Chikungunya virus (S27)</name>
                <number_unique_components>1</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>S27</sci_species_strain>
                <natural_host database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>VERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <virus_shell shell_id="1">
                    <diameter units="&#8491;">680</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>
            </virus_supramolecule>
        </supramolecule_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>7.4</ph>
                        <details>20 mM HEPES, 150 mM NaCl</details>
                    </buffer>
                    <grid>
                        <details>Quantifoil copper grids (R2/1, 200 mesh)</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <chamber_temperature units="K">120</chamber_temperature>
                        <instrument>FEI VITROBOT MARK III</instrument>
                        <method>Blot for 2.5 seconds before plunging.</method>
                    </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>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_cs units="mm">2.0</nominal_cs>
                    <nominal_defocus_min units="&#181;m">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.0</nominal_defocus_max>
                    <nominal_magnification>80000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">100</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 150,000 times magnification.</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2013-09-25</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">TVIPS TEMCAM-F816 (8k x 8k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">15.6</sampling_interval>
                            </digitization_details>
                            <number_real_images>350</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">18</average_electron_dose_per_image>
                            <bits_per_pixel>32.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Particle images were automatically boxed out using the program ethan.</details>
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">15.3</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Relion_1.3</name>
                        </software>
                    </software_list>
                    <number_images_used>5510</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="182251">
        <file>emd_6466.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>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>360</x>
            <y>360</y>
            <z>360</z>
        </spacing>
        <cell>
            <a units="&#8491;">1130.4</a>
            <b units="&#8491;">1130.4</b>
            <c units="&#8491;">1130.4</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>-0.02787305</minimum>
            <maximum>0.07516</maximum>
            <average>0.00221255</average>
            <std>0.01082234</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">3.14</x>
            <y units="&#8491;">3.14</y>
            <z units="&#8491;">3.14</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.038</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of CHIKV virus-like particle</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6466::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3J2W</access_code>
                    <chain>
                        <chain_id>B</chain_id>
                    </chain>
                    <chain>
                        <chain_id>C</chain_id>
                    </chain>
                    <chain>
                        <chain_id>D</chain_id>
                    </chain>
                    <chain>
                        <chain_id>N</chain_id>
                    </chain>
                    <chain>
                        <chain_id>O</chain_id>
                    </chain>
                    <chain>
                        <chain_id>P</chain_id>
                    </chain>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <details>The fitting was done manually first, then with "Fit in Map" in Chimera.</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>