<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://ftp.ebi.ac.uk/pub/databases/em_ebi/emdb_related/emdb-schemas/emdb_schemas/v3/v3_0_11_0/emdb.xsd" version="3.0.11.0" emdb_id="EMD-21867">
    <admin>
        <current_status>
            <date>2025-05-14</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <revision_history>
            <revision version="1.0" date="2020-07-29">
                <change_list>
                    <image>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </image>
                    <primary_map>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </primary_map>
                </change_list>
            </revision>
            <revision version="1.1" date="2025-05-14">
                <change_list>
                    <metadata>
                        <revision_group>EXPERIMENTAL_SUMMARY</revision_group>
                        <categories>
                            <category>em_admin</category>
                            <category>em_software</category>
                        </categories>
                        <items>
                            <item>_em_admin.last_update</item>
                            <item>_em_software.name</item>
                        </items>
                    </metadata>
                </change_list>
            </revision>
            <revision version="1.2" date="2024-05-29">
                <change_list>
                    <model>
                        <revision_group>DATA_COLLECTION</revision_group>
                        <categories>
                            <category>chem_comp_atom</category>
                            <category>chem_comp_bond</category>
                        </categories>
                    </model>
                </change_list>
            </revision>
            <revision version="1.3" date="2025-05-14">
                <change_list>
                    <model>
                        <revision_group>STRUCTURE_SUMMARY</revision_group>
                        <categories>
                            <category>em_admin</category>
                            <category>em_software</category>
                            <category>pdbx_entry_details</category>
                        </categories>
                        <items>
                            <item>_em_admin.last_update</item>
                            <item>_em_software.name</item>
                        </items>
                    </model>
                </change_list>
            </revision>
        </revision_history>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2020-04-28</deposition>
            <header_release>2020-07-29</header_release>
            <map_release>2020-07-29</map_release>
            <update>2025-05-14</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>R35GM122510</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Cryo-EM of the S. solfataricus rod-shaped virus, SSRV1</title>
        <authors_list>
            <author>Wang F</author>
            <author>Baquero DP</author>
        </authors_list>
        <keywords>helical symmetry, archaeal virus, rod-like virus, structural protein, VIRUS</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Wang F</author>
                    <author order="2">Baquero DP</author>
                    <author order="3">Beltran LC</author>
                    <author order="4">Su Z</author>
                    <author order="5">Osinski T</author>
                    <author order="6">Zheng W</author>
                    <author order="7">Prangishvili D</author>
                    <author order="8">Krupovic M</author>
                    <author order="9">Egelman EH</author>
                    <title>Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments.</title>
                    <journal_abbreviation>Proc.Natl.Acad.Sci.USA</journal_abbreviation>
                    <country>US</country>
                    <volume>117</volume>
                    <first_page>19643</first_page>
                    <last_page>19652</last_page>
                    <year>2020</year>
                    <external_references type="PUBMED">32759221</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.2011125117</external_references>
                    <external_references type="ISSN">1091-6490</external_references>
                    <external_references type="CSD">0040</external_references>
                    <external_references type="ASTM">PNASA6</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-21868</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>Cryo-EM of the S. islandicus filamentous virus, SIFV</details>
            </emdb_reference>
        </emdb_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6wq0</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>S. solfataricus rod-shaped virus, SSRV1</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>unclassified Rudivirus</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>3</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <sci_species_name ncbi="351054">unclassified Rudivirus</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="2287">Saccharolobus solfataricus</organism>
                </natural_host>
                <virus_type>VIRION</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
            </virus_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <dna macromolecule_id="1">
                <name>DNA (301-MER)</name>
                <natural_source database="NCBI">
                    <organism ncbi="351054">unclassified Rudivirus</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.092878148</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <sequence>
                    <string>(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)
(DA)</string>
                </sequence>
                <classification>DNA</classification>
            </dna>
            <dna macromolecule_id="2">
                <name>DNA (301-MER)</name>
                <natural_source database="NCBI">
                    <organism ncbi="351054">unclassified Rudivirus</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.092869141</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <sequence>
                    <string>(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)
(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)
(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)
(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)
(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)
(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)
(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)
(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)
(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)
(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)
(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)
(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)
(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)
(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)
(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)
(DT)</string>
                </sequence>
                <classification>DNA</classification>
            </dna>
            <protein_or_peptide macromolecule_id="3">
                <name>Structural protein</name>
                <natural_source database="NCBI">
                    <organism ncbi="351054">unclassified Rudivirus</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.014207112999999999</theoretical>
                </molecular_weight>
                <number_of_copies>46</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MAKGRTPRSFSQRYGKWNAKFTAFSNPTVASTILTNVAPIAQGNFQTNVPKFTSVNEQVSAVLTQYGVTGPSRAIYQGYG
LKVARALNRIGAGPALTNMVAGLKAYYVSAYGANPEILDAVTNIILGSPTGYVS</string>
                </sequence>
            </protein_or_peptide>
        </macromolecule_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>
                        <ph>6.0</ph>
                    </buffer>
                    <grid>
                        <details>unspecified</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                    </vitrification>
                </helical_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <helical_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>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K3 (6k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">50.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </helical_microscopy>
            </microscopy_list>
            <helical_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="Å">2.94</delta_z>
                            <delta_phi units="deg">24.53</delta_phi>
                            <axial_symmetry>D1</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">2.8</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <details>MODEL:MAP FSC, D99, MAP:MAP FSC</details>
                    <number_images_used>470000</number_images_used>
                </final_reconstruction>
                <ctf_correction>
                    <type>PHASE FLIPPING AND AMPLITUDE CORRECTION</type>
                </ctf_correction>
                <startup_model type_of_model="OTHER">
                    <details>averaged cylinder using all segments, with random azimuthal angles</details>
                </startup_model>
                <final_angle_assignment>
                    <type>NOT APPLICABLE</type>
                </final_angle_assignment>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="131073">
        <file>emd_21867.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>320</col>
            <row>320</row>
            <sec>320</sec>
        </dimensions>
        <origin>
            <col>-160</col>
            <row>-160</row>
            <sec>-160</sec>
        </origin>
        <spacing>
            <x>320</x>
            <y>320</y>
            <z>320</z>
        </spacing>
        <cell>
            <a units="Å">345.6</a>
            <b units="Å">345.6</b>
            <c units="Å">345.6</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>-0.15122311</minimum>
            <maximum>0.3060178</maximum>
            <average>0.000594526</average>
            <std>0.019977992</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.08</x>
            <y units="Å">1.08</y>
            <z units="Å">1.08</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0412</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-21867::::</label>
        <annotation_details>Cryo-EM of the S. solfataricus rod-shaped virus, SSRV1</annotation_details>
    </map>
</emd>
