<emd emdb_id="EMD-5671" 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>2013-05-10</deposition>
            <header_release>2013-07-03</header_release>
            <map_release>2013-12-11</map_release>
            <update>2013-12-18</update>
        </key_dates>
        <title>Cross-Neutralizing Human Anti-Poliovirus Antibodies Bind the Recognition Site for Cellular Receptor</title>
        <authors_list>
            <author>Chen Z</author>
            <author>Fischer ER</author>
            <author>Kouiavskaia D</author>
            <author>Hansen BT</author>
            <author>Ludtke SJ</author>
            <author>Bidzhieva B</author>
            <author>Makiya M</author>
            <author>Purcell RH</author>
            <author>Chumakov K</author>
        </authors_list>
        <keywords>Polio, Type 2 Polio, A12,</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Chen Z</author>
                    <author order="2">Fischer ER</author>
                    <author order="3">Kouiavskaia D</author>
                    <author order="4">Hansen BT</author>
                    <author order="5">Ludtke SJ</author>
                    <author order="6">Bidzhieva B</author>
                    <author order="7">Makiya M</author>
                    <author order="8">Agulto L</author>
                    <author order="9">Purcell RH</author>
                    <author order="10">Chumakov K</author>
                    <title>Cross-neutralizing human anti-poliovirus antibodies bind the recognition site for cellular receptor.</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <volume>110</volume>
                    <first_page>20242</first_page>
                    <last_page>20247</last_page>
                    <year>2013</year>
                    <external_references type="PUBMED">24277851</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1320041110</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Fab Fragment of A12 antibody bound to Type 2 poliovirus</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Fab Fragment of A12 antibody bound to Type 2 poliovirus</name>
                <number_unique_components>2</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name>Human poliovirus 2</name>
                <sci_species_name ncbi="12083">Human poliovirus 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_type>VIRION</virus_type>
                <virus_isolate>SPECIES</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">
                    <concentration units="mg/mL">1</concentration>
                    <grid>
                        <details>4 uL aliquots of sample were applied to freshly glow-discharged 200 mesh r2/2 Quantifoil copper grids suspended by forceps in the FEI Mark IV Vitrobot.</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">80</chamber_humidity>
                        <chamber_temperature units="K">65</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>Specimens were vitrified, after blotting for 2 seconds with a blot force of 5 at 80% relative humidity, by plunge freezing into liquid ethane.</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">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">5.0</nominal_defocus_max>
                    <nominal_magnification>47000.0</nominal_magnification>
                    <calibrated_magnification>80173.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">64</temperature_min>
                        <temperature_max units="K">66</temperature_max>
                        <temperature_average units="K">65</temperature_average>
                    </temperature>
                    <date>2011-03-03</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GENERIC CCD</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">2</sampling_interval>
                            </digitization_details>
                            <number_real_images>150</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>Liquid Nitrogen cooled</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Particles with a defocus range of 1-5 um were boxed with EMAN2, and then processed using the standard single particle reconstruction procedure with full CTF correction.</details>
                <ctf_correction>
                    <details>each image</details>
                </ctf_correction>
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">20.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN2</name>
                        </software>
                    </software_list>
                    <number_images_used>1500</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>10</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="52883">
        <file>emd_5671.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>239</col>
            <row>237</row>
            <sec>239</sec>
        </dimensions>
        <origin>
            <col>41</col>
            <row>42</row>
            <sec>41</sec>
        </origin>
        <spacing>
            <x>237</x>
            <y>239</y>
            <z>239</z>
        </spacing>
        <cell>
            <a units="&#8491;">430.19998</a>
            <b units="&#8491;">426.59998</b>
            <c units="&#8491;">430.19998</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>0.0</minimum>
            <maximum>2.1542964</maximum>
            <average>0.25201949</average>
            <std>0.45818526</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.8</x>
            <y units="&#8491;">1.8</y>
            <z units="&#8491;">1.8</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.7</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Cryo-EM reconstruction of type 2 polio virus with A12 Fab attached</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5671::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>1EAH</access_code>
                    <chain>
                        <chain_id>A</chain_id>
                    </chain>
                    <chain>
                        <chain_id>B</chain_id>
                    </chain>
                    <chain>
                        <chain_id>C</chain_id>
                    </chain>
                    <chain>
                        <chain_id>D</chain_id>
                    </chain>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>