<emd emdb_id="EMD-1986" 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>2011-11-11</deposition>
            <header_release>2011-11-17</header_release>
            <map_release>2011-11-17</map_release>
            <update>2012-10-10</update>
        </key_dates>
        <title>CryoEM reconstruction of the Marburg virus nucleocapsid.</title>
        <authors_list>
            <author>Bharat TAM</author>
            <author>Riches JD</author>
            <author>Kolesnikova L</author>
            <author>Welsch S</author>
            <author>Kraehling V</author>
            <author>Davey N</author>
            <author>Parsy ML</author>
            <author>Becker S</author>
            <author>Briggs JAG</author>
        </authors_list>
        <keywords>Marburg,virus,nucleocapsid,Nucleoprotein,VP24,VP35</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Bharat TAM</author>
                    <author order="2">Riches JD</author>
                    <author order="3">Kolesnikova L</author>
                    <author order="4">Welsch S</author>
                    <author order="5">Davey N</author>
                    <author order="6">Parsy ML</author>
                    <author order="7">Becker S</author>
                    <author order="8">Briggs JAG</author>
                    <title>Cryo-electron tomography of Marburg virus particles and their morphogenesis within infected cells.</title>
                    <journal>PLOS BIOL.</journal>
                    <volume>9</volume>
                    <first_page>e1001196</first_page>
                    <last_page>e1001196</last_page>
                    <year>2011</year>
                    <external_references type="PUBMED">22110401</external_references>
                    <external_references type="DOI">doi:10.1371/journal.pbio.1001196</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Marburg virus nucleocapsid</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Marburg virus nucleocapsid</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="Marburg virus">Marburg marburgvirus</name>
                <sci_species_name ncbi="11269">Marburg marburgvirus</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>STRAIN</virus_isolate>
                <virus_enveloped>true</virus_enveloped>
                <virus_empty>false</virus_empty>
                <syn_species_name>Marburg virus</syn_species_name>
            </virus_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>helical</method>
            <aggregation_state>filament</aggregation_state>
            <specimen_preparation_list>
                <helical_preparation preparation_id="1">
                    <buffer>
                        <details>PBS buffer with 4% PFA.</details>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <details>Vitrification instrument: Plunge freezer</details>
                        <method>Plunge freezing</method>
                    </vitrification>
                </helical_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <helical_microscopy microscopy_id="1">
                    <microscope>FEI/PHILIPS CM120T</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <nominal_cs units="mm">6.3</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.0006</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">0.004</nominal_defocus_max>
                    <nominal_magnification>37000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>ZEISS SCAI</scanner>
                                <sampling_interval units="&#181;m">14</sampling_interval>
                            </digitization_details>
                            <average_electron_dose_per_image units="e/&#8491;^2">10</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Gatan 626</specimen_holder>
                    <tilt_angle_min>0</tilt_angle_min>
                    <tilt_angle_max>0</tilt_angle_max>
                </helical_microscopy>
            </microscopy_list>
            <helical_processing image_processing_id="1">
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">5.0</delta_z>
                            <delta_phi units="deg">24.3</delta_phi>
                        </helical_parameters>
                    </applied_symmetry>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">25.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>Spider, Bsoft</name>
                        </software>
                    </software_list>
                </final_reconstruction>
                <ctf_correction>
                    <details>Phase flip</details>
                </ctf_correction>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="7912">
        <file>emd_1986.map.gz</file>
        <symmetry>
            <space_group>0</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>150</col>
            <row>150</row>
            <sec>90</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>150</x>
            <y>150</y>
            <z>90</z>
        </spacing>
        <cell>
            <a units="&#8491;">600</a>
            <b units="&#8491;">600</b>
            <c units="&#8491;">360</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>-0.00187585</minimum>
            <maximum>0.00387182</maximum>
            <average>0.00040353</average>
            <std>0.000906448</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">4</x>
            <y units="&#8491;">4</y>
            <z units="&#8491;">4</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.00124</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>This is a map of the Marburg virus nucleocapsid within virions.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-1986::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>2WYY</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <details>Protocol: Rigid body. 4 monomers from the VSV Nucleoprotein structure were fitted in as a single rigid body without any corrections.</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>