<emd emdb_id="EMD-5422" 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>2012-05-14</deposition>
            <header_release>2012-05-16</header_release>
            <map_release>2012-05-16</map_release>
            <update>2016-10-12</update>
        </key_dates>
        <title>cryo-EM reconstruction of immature dengue virus</title>
        <authors_list>
            <author>Zhang Y</author>
            <author>Zhang W</author>
            <author>Ogata S</author>
            <author>Clements D</author>
            <author>Strauss JH</author>
            <author>Baker TS</author>
            <author>Kuhn RJ</author>
            <author>Rossmann MG</author>
        </authors_list>
        <keywords>immature dengue flavivirus cryo-EM</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Zhang Y</author>
                    <author order="2">Zhang W</author>
                    <author order="3">Ogata S</author>
                    <author order="4">Clements D</author>
                    <author order="5">Strauss JH</author>
                    <author order="6">Baker TS</author>
                    <author order="7">Kuhn RJ</author>
                    <author order="8">Rossmann MG</author>
                    <title>Conformational changes of the flavivirus E glycoprotein.</title>
                    <journal>STRUCTURE</journal>
                    <volume>12</volume>
                    <first_page>1607</first_page>
                    <last_page>1618</last_page>
                    <year>2004</year>
                    <external_references type="PUBMED">15341726</external_references>
                    <external_references type="DOI">doi:10.1016/j.str.2004.06.019</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>1tge</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>immature dengue particle</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>immature dengue particle</name>
                <oligomeric_state>icosahedral</oligomeric_state>
                <number_unique_components>3</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name>Dengue virus 2</name>
                <details>Dengue virus 2 strain PR159-S1</details>
                <sci_species_name ncbi="11060">Dengue virus 2</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="7160">Aedes albopictus</organism>
                    <synonym_organism>INVERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <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">
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <details>Vitrification instrument: Purdue-manufactured, gravity-driven device. Vitrification carried out in hood.</details>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI/PHILIPS CM300FEG/T</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>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <date>2003-02-01</date>
                    <image_recording_list>
                        <image_recording>
                            <digitization_details>
                                <scanner>ZEISS SCAI</scanner>
                            </digitization_details>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">12.5</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <number_images_used>4099</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="53442">
        <file>emd_5422.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>301</col>
            <row>301</row>
            <sec>151</sec>
        </dimensions>
        <origin>
            <col>-150</col>
            <row>-150</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>301</x>
            <y>301</y>
            <z>151</z>
        </spacing>
        <cell>
            <a units="&#8491;">638.12</a>
            <b units="&#8491;">638.12</b>
            <c units="&#8491;">320.12</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
        </cell>
        <axis_order>
            <fast>Y</fast>
            <medium>X</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-3.10537338</minimum>
            <maximum>5.79204464</maximum>
            <average>-0.02588803</average>
            <std>1.00161886</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.12</x>
            <y units="&#8491;">2.12</y>
            <z units="&#8491;">2.12</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.25</level>
                <source>EMDB</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of immature dengue viral particles</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5422::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3C6D</access_code>
                </initial_model>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>