<emd emdb_id="EMD-5374" 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>2011-12-20</deposition>
            <header_release>2012-01-09</header_release>
            <map_release>2012-01-30</map_release>
            <update>2012-02-08</update>
        </key_dates>
        <title>Structural basis for broad detection of genogroup II noroviruses by a monoclonal antibody that binds to a site occluded in the viral particle</title>
        <authors_list>
            <author>Hansman GS</author>
            <author>Taylor DW</author>
            <author>McLellan JS</author>
            <author>Smith TJ</author>
            <author>Georgiev I</author>
            <author>Tame JRH</author>
            <author>Park SY</author>
            <author>Yamazaki M</author>
            <author>Gondaira F</author>
            <author>Miki M</author>
            <author>Katayama K</author>
            <author>Murata K</author>
            <author>Kwong PD</author>
        </authors_list>
        <keywords>norovirus</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Hansman GS</author>
                    <author order="2">Taylor DW</author>
                    <author order="3">McLellan JS</author>
                    <author order="4">Smith TJ</author>
                    <author order="5">Georgiev I</author>
                    <author order="6">Tame JR</author>
                    <author order="7">Park SY</author>
                    <author order="8">Yamazaki M</author>
                    <author order="9">Gondaira F</author>
                    <author order="10">Miki M</author>
                    <author order="11">Katayama K</author>
                    <author order="12">Murata K</author>
                    <author order="13">Kwong PD</author>
                    <title>Structural basis for broad detection of genogroup II noroviruses by a monoclonal antibody that binds to a site occluded in the viral particle.</title>
                    <journal>J.VIROL.</journal>
                    <volume>86</volume>
                    <first_page>3635</first_page>
                    <last_page>3646</last_page>
                    <year>2012</year>
                    <external_references type="PUBMED">22278249</external_references>
                    <external_references type="DOI">doi:10.1128/JVI.06868-11</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>GII.10 norovirus VLP</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>GII.10 norovirus VLP</name>
                <oligomeric_state>icosahedral (T3)</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">10</experimental>
                    <theoretical units="MDa">10</theoretical>
                </molecular_weight>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="GII.10 Vietnam 026 VLP">Norovirus genogroup GII.10</name>
                <sci_species_name ncbi="747305">Norovirus genogroup GII.10</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">10</experimental>
                    <theoretical units="MDa">10</theoretical>
                </molecular_weight>
                <virus_shell shell_id="1">
                    <triangulation>3</triangulation>
                </virus_shell>
                <virus_type>VIRUS-LIKE PARTICLE</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>true</virus_empty>
                <syn_species_name>GII.10 Vietnam 026 VLP</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">1.0</concentration>
                    <buffer>
                        <ph>7.3</ph>
                        <details>PBS</details>
                    </buffer>
                    <grid>
                        <details>Quantifoil R1.2/1.3 Mo 200 mesh</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <details>Vitrification instrument: FEI Vitrobot Mark IV. Quantifoil Mo 200 mesh holey carbon grid with a thin layer of carbon over the holes</details>
                        <method>automatic blotting for 8 seconds</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 2200FS</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">0.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.0</nominal_defocus_max>
                    <nominal_magnification>40000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <date>2011-07-22</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GENERIC TVIPS (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Gatan</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>The particles were selected semi-automatically using the swarm program in EMAN2.</details>
                <ctf_correction>
                    <details>Each image</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>EMAN2</name>
                        </software>
                    </software_list>
                    <number_images_used>8000</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="61037">
        <file>emd_5374.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>250</col>
            <row>250</row>
            <sec>250</sec>
        </dimensions>
        <origin>
            <col>-125</col>
            <row>-125</row>
            <sec>-125</sec>
        </origin>
        <spacing>
            <x>250</x>
            <y>250</y>
            <z>250</z>
        </spacing>
        <cell>
            <a units="&#8491;">600.0</a>
            <b units="&#8491;">600.0</b>
            <c units="&#8491;">600.0</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>-6.03285646</minimum>
            <maximum>14.81038094</maximum>
            <average>0.0</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.4</x>
            <y units="&#8491;">2.4</y>
            <z units="&#8491;">2.4</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.87</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Surface rendering of GII.10 norovirus VLP</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5374::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_5374.png</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>