<emd emdb_id="EMD-5117" 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>2009-06-01</deposition>
            <header_release>2009-08-20</header_release>
            <map_release>2009-10-01</map_release>
            <update>2011-09-27</update>
        </key_dates>
        <title>Structure of furin-cleaved immature dengue virus at low pH</title>
        <authors_list>
            <author>Yu I</author>
            <author>Holdaway HA</author>
            <author>Chipman PR</author>
            <author>Kuhn RJ</author>
            <author>Rossmann MG</author>
            <author>Chen J</author>
        </authors_list>
        <keywords>dengue,prM,E,furin,maturation</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Yu IM</author>
                    <author order="2">Holdaway HA</author>
                    <author order="3">Chipman PR</author>
                    <author order="4">Kuhn RJ</author>
                    <author order="5">Rossmann MG</author>
                    <author order="6">Chen J</author>
                    <title>Association of the pr peptides with dengue virus at acidic pH blocks membrane fusion.</title>
                    <journal>J.VIROL.</journal>
                    <volume>83</volume>
                    <first_page>12101</first_page>
                    <last_page>12107</last_page>
                    <year>2009</year>
                    <external_references type="PUBMED">19759134</external_references>
                    <external_references type="DOI">doi:10.1128/JVI.01637-09</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3iya</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Immature dengue virus at low pH after furin cleavage</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Immature dengue virus at low pH after furin cleavage</name>
                <number_unique_components>2</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="dengue">Dengue virus</name>
                <sci_species_name ncbi="12637">Dengue virus</sci_species_name>
                <natural_host database="NCBI">
                    <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>
                <syn_species_name>dengue</syn_species_name>
            </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>6.0</ph>
                        <details>6 mM Tris-HCL, 25 mM MES, 120 mM NaCl, 1 mM EDTA</details>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>OTHER</instrument>
                        <method>A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI/PHILIPS CM200FEG</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_defocus_min units="&#181;m">1.8</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.8</nominal_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <date>2008-06-13</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN MULTISCAN</film_or_detector_model>
                            <number_real_images>45</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">25</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Eucentric</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">22.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EM3DR</name>
                        </software>
                    </software_list>
                    <number_images_used>635</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="9612">
        <file>emd_5117.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>135</col>
            <row>135</row>
            <sec>135</sec>
        </dimensions>
        <origin>
            <col>-67</col>
            <row>-67</row>
            <sec>-67</sec>
        </origin>
        <spacing>
            <x>135</x>
            <y>135</y>
            <z>135</z>
        </spacing>
        <cell>
            <a units="&#8491;">594</a>
            <b units="&#8491;">594</b>
            <c units="&#8491;">594</c>
            <alpha units="deg">90</alpha>
            <beta units="deg">90</beta>
            <gamma units="deg">90</gamma>
        </cell>
        <axis_order>
            <fast>X</fast>
            <medium>Y</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-261.408999999999992</minimum>
            <maximum>840.423000000000002</maximum>
            <average>100.468000000000004</average>
            <std>232.090000000000003</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">4.4</x>
            <y units="&#8491;">4.4</y>
            <z units="&#8491;">4.4</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>200.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Immature dengue virus after furin cleavage at low pH</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5117::::</details>
    </map>
</emd>