<emd emdb_id="EMD-2369" 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>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2013-04-25</deposition>
            <header_release>2013-05-08</header_release>
            <map_release>2013-05-29</map_release>
            <update>2013-07-24</update>
        </key_dates>
        <title>The Respiratory Syncytial Virus nucleoprotein-RNA complex forms a left-handed helical nucleocapsid.</title>
        <authors_list>
            <author>Bakker SE</author>
            <author>Duquerroy S</author>
            <author>Galloux M</author>
            <author>Loney C</author>
            <author>Conner E</author>
            <author>Eleouet JF</author>
            <author>Rey FA</author>
            <author>Bhella D</author>
        </authors_list>
        <keywords>Respiratory Syncytial Virus, nucleocapsid, cryo-electron tomography, sub-tomogram averaging</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Bakker SE</author>
                    <author order="2">Duquerroy S</author>
                    <author order="3">Galloux M</author>
                    <author order="4">Loney C</author>
                    <author order="5">Conner E</author>
                    <author order="6">Eleouet JF</author>
                    <author order="7">Rey FA</author>
                    <author order="8">Bhella D</author>
                    <title>The respiratory syncytial virus nucleoprotein-RNA complex forms a left-handed helical nucleocapsid.</title>
                    <journal>J.GEN.VIROL.</journal>
                    <volume>94</volume>
                    <first_page>1734</first_page>
                    <last_page>1738</last_page>
                    <year>2013</year>
                    <external_references type="PUBMED">23677789</external_references>
                    <external_references type="DOI">doi:10.1099/vir.0.053025-0</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>4bkk</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Purified recombinant RSV nucleocapsids.</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Purified recombinant RSV nucleocapsids.</name>
                <oligomeric_state>variable helices</oligomeric_state>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="RSV">Respiratory syncytial virus</name>
                <details>Purified recombinant nucleocapsid</details>
                <sci_species_name ncbi="12814">Respiratory syncytial virus</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>VERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI">
                    <recombinant_organism ncbi="7108">Spodoptera frugiperda</recombinant_organism>
                    <recombinant_cell>Sf21</recombinant_cell>
                    <recombinant_plasmid>Rbac69</recombinant_plasmid>
                </host_system>
                <virus_type>OTHER</virus_type>
                <virus_isolate>OTHER</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
                <syn_species_name>RSV</syn_species_name>
            </virus_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>subtomogramAveraging</method>
            <aggregation_state>filament</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <ph>7.4</ph>
                        <details>50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 10 mM EDTA</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>Protein preparations were mixed with 10 nm colloidal gold and loaded onto freshly glow-discharged perforated C-flat carbon films (CF-22-2C, Protochips Inc.). Grids were then washed in 0.1% trehalose, and stained using 5% ammonium molybdate (pH 7.4) and 0.1% trehalose, drained and allowed to dry in air</details>
                    </staining>
                    <grid>
                        <details>Glow-discharged perforated C-flat carbon films (CF-22-2C, Protochips Inc.)</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>NONE</cryogen_name>
                        <instrument>OTHER</instrument>
                    </vitrification>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_microscopy microscopy_id="1">
                    <microscope>JEOL 2200FSC</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_cs units="mm">2.0</nominal_cs>
                    <nominal_defocus_min units="&#181;m">2.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">4.0</nominal_defocus_max>
                    <nominal_magnification>40000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">97</temperature_min>
                        <temperature_max units="K">293</temperature_max>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Corrected at 100k times mag in digital micrograph</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <specialist_optics>
                        <energy_filter>
                            <name>Jeol</name>
                            <lower_energy_threshold units="eV">0.0</lower_energy_threshold>
                            <upper_energy_threshold units="eV">30.0</upper_energy_threshold>
                        </energy_filter>
                    </specialist_optics>
                    <details>Room temperature stained grids imaged at LN2 temperatures.</details>
                    <date>2010-07-15</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <number_real_images>9</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">131</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">-60</min_angle>
                            <max_angle units="deg">60</max_angle>
                        </axis1>
                    </tilt_series>
                </subtomogram_averaging_microscopy>
            </microscopy_list>
            <subtomogram_averaging_processing image_processing_id="1">
                <details>Subtomograms were manually picked. A starting model was obtained by manually aligning 100 subtomograms, all subtomograms were aligned to this starting model. To mitigate missing wedge artefacts, the orientations around the helical axis were randomised before further alignment.</details>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <software_list>
                        <software>
                            <name>Etomo, Dynamo</name>
                        </software>
                    </software_list>
                    <details>Subtomograms were picked from nine tomograms.</details>
                    <number_subtomograms_used>911</number_subtomograms_used>
                </final_reconstruction>
                <final_three_d_classification>
                    <number_classes>1</number_classes>
                </final_three_d_classification>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="1025">
        <file>emd_2369.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>64</col>
            <row>64</row>
            <sec>64</sec>
        </dimensions>
        <origin>
            <col>-32</col>
            <row>-32</row>
            <sec>-32</sec>
        </origin>
        <spacing>
            <x>64</x>
            <y>64</y>
            <z>64</z>
        </spacing>
        <cell>
            <a units="&#8491;">416.0</a>
            <b units="&#8491;">416.0</b>
            <c units="&#8491;">416.0</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>-2.29873204</minimum>
            <maximum>1.89033198</maximum>
            <average>-0.0025243</average>
            <std>0.4238916</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">6.5</x>
            <y units="&#8491;">6.5</y>
            <z units="&#8491;">6.5</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.66</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Sub-tomogram average of purified RSV nucleocapsid</annotation_details>
        <details>::::EMDATABANK.org::::EMD-2369::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>2WJ8</access_code>
                </initial_model>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>