<emd emdb_id="EMD-5499" 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>2012-09-26</deposition>
            <header_release>2012-11-28</header_release>
            <map_release>2012-12-19</map_release>
            <update>2013-01-16</update>
        </key_dates>
        <title>CryoEM structure of Dengue virus, partial map</title>
        <authors_list>
            <author>Zhang X</author>
            <author>Ge P</author>
            <author>Yu X</author>
            <author>Brannan JM</author>
            <author>Bi G</author>
            <author>Zhang Q</author>
            <author>Schein S</author>
            <author>Zhou ZH</author>
        </authors_list>
        <keywords>flavivirus, fusion protein, protein complex, membrane</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Zhang X</author>
                    <author order="2">Ge P</author>
                    <author order="3">Yu X</author>
                    <author order="4">Brannan JM</author>
                    <author order="5">Bi G</author>
                    <author order="6">Zhang Q</author>
                    <author order="7">Schein S</author>
                    <author order="8">Zhou ZH</author>
                    <title>Cryo-EM structure of the mature dengue virus at 3.5-A resolution.</title>
                    <journal>NAT.STRUCT.MOL.BIOL.</journal>
                    <volume>20</volume>
                    <first_page>105</first_page>
                    <last_page>110</last_page>
                    <year>2013</year>
                    <external_references type="PUBMED">23241927</external_references>
                    <external_references type="DOI">doi:10.1038/nsmb.2463</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3j2p</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Dengue Virus 2</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Dengue Virus 2</name>
                <oligomeric_state>E:M:M:E hetero-tetramer</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">0.125</theoretical>
                </molecular_weight>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name>Dengue virus 2</name>
                <sci_species_name ncbi="11060">Dengue virus 2</sci_species_name>
                <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">
                    <triangulation>3</triangulation>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>true</virus_enveloped>
                <virus_empty>false</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">
                    <buffer>
                        <ph>7.4</ph>
                        <details>50 mM Tris, 140 mM NaCl, 5 mM EDTA</details>
                    </buffer>
                    <grid>
                        <details>Quantifoil R2/1</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <method>2.5 uL sample added per grid</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">2.7</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.4</nominal_defocus_max>
                    <nominal_magnification>59000.0</nominal_magnification>
                    <calibrated_magnification>57518.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>software compensation</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2010-12-23</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>NIKON SUPER COOLSCAN 9000</scanner>
                                <sampling_interval units="&#181;m">6.35</sampling_interval>
                            </digitization_details>
                            <number_real_images>1103</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">25</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>EMAN with Multi-path Simulated Annealing</details>
                <ctf_correction>
                    <details>EMAN per particle, with astigmatism compensation</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">3.6</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN</name>
                        </software>
                    </software_list>
                    <number_images_used>9288</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="9001">
        <file>emd_5499.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>120</col>
            <row>160</row>
            <sec>120</sec>
        </dimensions>
        <origin>
            <col>-190</col>
            <row>-175</row>
            <sec>-155</sec>
        </origin>
        <spacing>
            <x>160</x>
            <y>120</y>
            <z>120</z>
        </spacing>
        <cell>
            <a units="&#8491;">132.48</a>
            <b units="&#8491;">176.64</b>
            <c units="&#8491;">132.48</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>-17.318016050000001</minimum>
            <maximum>24.021337509999999</maximum>
            <average>0.10023053</average>
            <std>2.33172154</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.104</x>
            <y units="&#8491;">1.104</y>
            <z units="&#8491;">1.104</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>4.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>3-fold averaged Dengue virus capsid E:M:M:E hetero-dimer</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5499::::</details>
    </map>
</emd>