<emd emdb_id="EMD-1445" 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>2007-10-22</deposition>
            <header_release>2007-10-25</header_release>
            <map_release>2008-10-25</map_release>
            <update>2012-10-24</update>
        </key_dates>
        <title>Cryo-electron tomography of Kaposi's sarcoma-associated herpesvirus capsids reveals dynamic scaffolding structures essential to capsid assembly and maturation.</title>
        <authors_list>
            <author>Deng B</author>
            <author>O'Connor CM</author>
            <author>Kedes DH</author>
            <author>Zhou ZH</author>
        </authors_list>
        <keywords />
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Deng B</author>
                    <author order="2">O'Connor CM</author>
                    <author order="3">Kedes DH</author>
                    <author order="4">Zhou ZH</author>
                    <title>Cryo-electron tomography of Kaposi's sarcoma-associated herpesvirus capsids reveals dynamic scaffolding structures essential to capsid assembly and maturation.</title>
                    <journal>J.STRUCT.BIOL.</journal>
                    <volume>161</volume>
                    <first_page>419</first_page>
                    <last_page>427</last_page>
                    <year>2008</year>
                    <external_references type="PUBMED">18164626</external_references>
                    <external_references type="DOI">doi:10.1016/j.jsb.2007.10.016</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>KSHV</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>KSHV</name>
                <oligomeric_state>1</oligomeric_state>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="Kaposi's sarcoma-associated herpesvirus, HHV-8">Human herpesvirus 8</name>
                <sci_species_name ncbi="37296">Human herpesvirus 8</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_shell shell_id="1">
                    <diameter units="&#8491;">1250</diameter>
                    <triangulation>16</triangulation>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>true</virus_empty>
                <syn_species_name>Kaposi's sarcoma-associated herpesvirus, HHV-8</syn_species_name>
            </virus_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>subtomogramAveraging</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <ph>7.4</ph>
                        <details>PBS</details>
                    </buffer>
                    <grid>
                        <details>holey carbon 300 mesh copper grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <details>Vitrification instrument: plunger</details>
                        <method>Blot for 1 seconds before plunging</method>
                    </vitrification>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F30</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</nominal_cs>
                    <nominal_defocus_min units="&#181;m">6.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">8.0</nominal_defocus_max>
                    <nominal_magnification>23000.0</nominal_magnification>
                    <calibrated_magnification>38200.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">90</temperature_min>
                        <temperature_max units="K">90</temperature_max>
                        <temperature_average units="K">90</temperature_average>
                    </temperature>
                    <details>Tilted from -70 to +70 with 2 degree interval.</details>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GENERIC CCD</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">1</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Side entry liquid nitrogen-cooled cryo specimen holder</specimen_holder>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">70</min_angle>
                            <max_angle units="deg">70</max_angle>
                        </axis1>
                    </tilt_series>
                </subtomogram_averaging_microscopy>
            </microscopy_list>
            <subtomogram_averaging_processing image_processing_id="1">
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">40.0</resolution>
                    <software_list>
                        <software>
                            <name>PROJALIGN</name>
                        </software>
                    </software_list>
                </final_reconstruction>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="18523">
        <file>emd_1445.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>168</col>
            <row>168</row>
            <sec>168</sec>
        </dimensions>
        <origin>
            <col>-84</col>
            <row>-84</row>
            <sec>-84</sec>
        </origin>
        <spacing>
            <x>168</x>
            <y>168</y>
            <z>168</z>
        </spacing>
        <cell>
            <a units="&#8491;">1320.14</a>
            <b units="&#8491;">1320.14</b>
            <c units="&#8491;">1320.14</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>-8.66982</minimum>
            <maximum>8.860939999999999</maximum>
            <average>0.0390897</average>
            <std>1.21987</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">7.858</x>
            <y units="&#8491;">7.858</y>
            <z units="&#8491;">7.858</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.38</level>
            </contour>
        </contour_list>
        <annotation_details>KSHV B capsid</annotation_details>
        <details>::::EMDATABANK.org::::EMD-1445::::</details>
    </map>
</emd>