<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_9/emdb.xsd" emdb_id="EMD-21133" version="3.0.1.9">
    <admin>
        <current_status>
            <date>2020-08-26</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-12-16</deposition>
            <header_release>2020-01-15</header_release>
            <map_release>2020-08-12</map_release>
            <update>2020-08-26</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Health and Medical Research Council (NHMRC, Australia)</funding_body>
                <code>APP1161916</code>
                <country>Australia</country>
            </grant_reference>
        </grant_support>
        <title>Cryo-EM SPA : Structure of the PCBP2/Stem Loop IVm complex underlying the functionality of the poliovirus type I IRES.</title>
        <authors_list>
            <author>Wilce MCJ</author>
            <author>Wilce JA</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Beckham SA</author>
                    <author order="2">Matak MY</author>
                    <author order="3">Belousoff MJ</author>
                    <author order="4">Venugopal H</author>
                    <author order="5">Shah N</author>
                    <author order="6">Vankadari N</author>
                    <author order="7">Elmlund H</author>
                    <author order="8">Nguyen JHC</author>
                    <author order="9">Semler BL</author>
                    <author order="10">Wilce MCJ</author>
                    <author order="11">Wilce JA</author>
                    <title>Structure of the PCBP2/stem-loop IV complex underlying translation initiation mediated by the poliovirus type I IRES.</title>
                    <journal_abbreviation>Nucleic Acids Res.</journal_abbreviation>
                    <country>UK</country>
                    <volume>48</volume>
                    <first_page>8006</first_page>
                    <last_page>8021</last_page>
                    <year>2020</year>
                    <external_references type="PUBMED">32556302</external_references>
                    <external_references type="DOI">doi:10.1093/nar/gkaa519</external_references>
                    <external_references type="ISSN">1362-4962</external_references>
                    <external_references type="CSD">0389</external_references>
                    <external_references type="ASTM">NARHAD</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-21133</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>truncated stem loop IV of the poliovirus IRES, residues, 278-398 in complex with PolyC binding protein 2</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>truncated stem loop IV of the poliovirus IRES, residues, 278-398 in complex with PolyC binding protein 2</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="12081">Poliovirus type 1 (strain Mahoney)</organism>
                    <strain>Mahoney</strain>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>PolyC Binding Protein 2</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MDTGVIEGGLNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIIT
LAGPTNAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKI
KEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVMLETLSQSPPKGVTI
PYRPKPSSSPVIFAGGQDRYSTGSDSASFPHTTPSMCLNPDLEGPPLEAYTIQGQYAIPQ
PDLTKLHQLAMQQSHFPMTHGNTGFSGIESSSPEVKGYWGLDASAQTTSHELTIPNDLIG
CIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSSETG
GMGSSLEHHHHHH</string>
                </sequence>
            </protein_or_peptide>
            <rna macromolecule_id="2">
                <name>Poliovirus (Mahoney) : truncated Stemloop IV from IRES</name>
                <natural_source database="NCBI">
                    <organism ncbi="12081">Poliovirus type 1 (strain Mahoney)</organism>
                    <strain>Mahoney</strain>
                </natural_source>
                <details>Produced using in vitro transcription : T7 RiboMAX (Promega)</details>
                <sequence>
                    <string>CGCGCGUUGCGCUCAGCACUCAACCCCAGAGUGUAGCUUAGGCUGAUGAGUCUGGACAUCCCUCACCGGUGACGGUGGUCCAGGCUGCGUUGGCGGCCUACCUAUGGCUAACGCCAUGGGACGCGCG</string>
                </sequence>
            </rna>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>singleParticle</method>
            <aggregation_state>twoDArray</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <concentration units="mg/mL">0.14</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>5 mM HEPES-KOH, 25 mM KCl, 2 mM MgCl2, 2 mM DTT, 4 % glycerol, 0.1 mM EDTA, pH 7.5</details>
                    </buffer>
                    <grid>
                        <model>Quantifoil R1.2/1.3</model>
                        <material>COPPER</material>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">298</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <details>2.5 second blot. </details>
                    </vitrification>
                    <details>A mono disperse sample was applied</details>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</microscope>
                    <illumination_mode>OTHER</illumination_mode>
                    <imaging_mode>OTHER</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <specialist_optics>
                        <phase_plate>VOLTA PHASE PLATE</phase_plate>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 QUANTUM (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">40.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>CTFFIND</name>
                            <processing_details>CTFFIND</processing_details>
                        </software>
                    </software_list>
                </ctf_correction>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <algorithm>FOURIER SPACE</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">6.1</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <number_images_used>888988</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="11944">
        <file>emd_21133.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>144</col>
            <row>144</row>
            <sec>144</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>144</x>
            <y>144</y>
            <z>144</z>
        </spacing>
        <cell>
            <a units="Å">152.63998</a>
            <b units="Å">152.63998</b>
            <c units="Å">152.63998</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>-0.06869157</minimum>
            <maximum>0.1436145</maximum>
            <average>0.0004524068</average>
            <std>0.0059334515</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.06</x>
            <y units="Å">1.06</y>
            <z units="Å">1.06</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.019</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-21133::::</label>
        <annotation_details>Structure of the PCBP2/Stem Loop</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>AB INITIO MODEL</refinement_protocol>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
