<emd emdb_id="EMD-5122" 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>2009-06-15</deposition>
            <header_release>2009-07-31</header_release>
            <map_release>2010-03-10</map_release>
            <update>2011-09-27</update>
        </key_dates>
        <title>RNA-releasing poliovirus intermediates</title>
        <authors_list>
            <author>Levy HC</author>
            <author>Bostina M</author>
            <author>Filman DJ</author>
            <author>Hogle JM</author>
        </authors_list>
        <keywords>Picornavirus, poliovirus, intermediate, RNA-release, 80S</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Levy HC</author>
                    <author order="2">Bostina M</author>
                    <author order="3">Filman DJ</author>
                    <author order="4">Hogle JM</author>
                    <title>Catching a virus in the act of RNA release: a novel poliovirus uncoating intermediate characterized by cryo-electron microscopy.</title>
                    <journal>J.VIROL.</journal>
                    <volume>84</volume>
                    <first_page>4426</first_page>
                    <last_page>4441</last_page>
                    <year>2010</year>
                    <external_references type="PUBMED">20181687</external_references>
                    <external_references type="DOI">doi:10.1128/JVI.02393-09</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3iyc</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>80S poliovirus</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>80S poliovirus</name>
                <details>native virus heat-treated at 56 degrees C</details>
                <oligomeric_state>60 promoters arranged as a icosahedron</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">8.3</experimental>
                    <theoretical units="MDa">8.3</theoretical>
                    <method>Sedimentation</method>
                </molecular_weight>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="poliovirus 1 mahoney">poliovirus 1 mahoney</name>
                <details>native virus is converted by heat-treatment to 80S</details>
                <sci_species_name>poliovirus 1 mahoney</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>VERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <molecular_weight>
                    <experimental units="MDa">8.3</experimental>
                    <theoretical units="MDa">8.3</theoretical>
                </molecular_weight>
                <virus_shell shell_id="1">
                    <name>capsid</name>
                    <diameter units="&#8491;">290</diameter>
                    <triangulation>1</triangulation>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>SEROTYPE</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>true</virus_empty>
                <syn_species_name>poliovirus 1 mahoney</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">
                    <concentration units="mg/mL">0.2</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <details>20mM Tris, 50mM NaCl, 2 mM CaCl2</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>not stained</details>
                    </staining>
                    <grid>
                        <details>200 mesh copper grids</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <details>Vitrification instrument: home made plunger</details>
                        <method>blot for 3 secs</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F30</microscope>
                    <illumination_mode>OTHER</illumination_mode>
                    <imaging_mode>OTHER</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_defocus_min units="&#181;m">0.9</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.0</nominal_defocus_max>
                    <nominal_magnification>59000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>ZEISS SCAI</scanner>
                                <sampling_interval units="&#181;m">7</sampling_interval>
                            </digitization_details>
                            <number_real_images>138</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">15</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">
                <details>10,000 particle were partitioned into two distinct classes</details>
                <ctf_correction>
                    <details>each micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">10.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>PFT2, EM3DR2</name>
                        </software>
                    </software_list>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="31723">
        <file>emd_5122.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>201</col>
            <row>201</row>
            <sec>201</sec>
        </dimensions>
        <origin>
            <col>-100</col>
            <row>-100</row>
            <sec>-100</sec>
        </origin>
        <spacing>
            <x>201</x>
            <y>201</y>
            <z>201</z>
        </spacing>
        <cell>
            <a units="&#8491;">466.782</a>
            <b units="&#8491;">466.782</b>
            <c units="&#8491;">466.782</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>-29.207799999999999</minimum>
            <maximum>68.046800000000005</maximum>
            <average>1.89523</average>
            <std>8.2149</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.3223</x>
            <y units="&#8491;">2.3223</y>
            <z units="&#8491;">2.3223</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>LATE early RNA-releasing 80S poliovirus</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5122::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>1pov</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>INSOUT</name>
                    </software>
                </software_list>
                <details>Protocol: Rigid Body</details>
                <refinement_space>RECIPROCAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>