<emd emdb_id="EMD-6428" 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>2015-08-16</deposition>
            <header_release>2015-09-09</header_release>
            <map_release>2015-09-09</map_release>
            <update>2016-02-17</update>
        </key_dates>
        <title>Cryo-EM structure of MAVS CARD C1 filament</title>
        <authors_list>
            <author>Xu H</author>
            <author>He X</author>
            <author>Zheng H</author>
            <author>Huang LJ</author>
            <author>Hou F</author>
            <author>Yu Z</author>
            <author>de la Cruz MJ</author>
            <author>Borkowski B</author>
            <author>Zhang X</author>
            <author>Chen ZJ</author>
            <author>Jiang Q-X</author>
        </authors_list>
        <keywords>Innate immunity, helical filament</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Xu H</author>
                    <author order="2">He X</author>
                    <author order="3">Zheng H</author>
                    <author order="4">Huang LJ</author>
                    <author order="5">Hou F</author>
                    <author order="6">Yu Z</author>
                    <author order="7">de la Cruz MJ</author>
                    <author order="8">Borkowski B</author>
                    <author order="9">Zhang X</author>
                    <author order="10">Chen ZJ</author>
                    <author order="11">Jiang QX</author>
                    <title>Correction: Structural basis for the prion-like MAVS filaments in antiviral innate immunity.</title>
                    <journal>eLife</journal>
                    <volume>4</volume>
                    <first_page>e07546</first_page>
                    <last_page>e07546</last_page>
                    <year>2015</year>
                    <external_references type="PUBMED">26314863</external_references>
                    <external_references type="DOI">doi:10.7554/eLife.07546</external_references>
                </journal_citation>
            </primary_citation>
            <secondary_citation>
                <journal_citation published="true">
                    <author order="1">Xu H</author>
                    <author order="2">He X</author>
                    <author order="3">Zheng H</author>
                    <author order="4">Huang LJ</author>
                    <author order="5">Hou F</author>
                    <author order="6">Yu Z</author>
                    <author order="7">de la Cruz MJ</author>
                    <author order="8">Borkowski B</author>
                    <author order="9">Zhang X</author>
                    <author order="10">Chen ZJ</author>
                    <author order="11">Jiang QX</author>
                    <title>Structural basis for the prion-like MAVS filaments in antiviral innate immunity.</title>
                    <journal>eLife</journal>
                    <volume>3</volume>
                    <first_page>e01489</first_page>
                    <last_page>e01489</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">24569476</external_references>
                    <external_references type="DOI">doi:10.7554/eLife.01489</external_references>
                </journal_citation>
            </secondary_citation>
        </citation_list>
        <auxiliary_link_list>
            <auxiliary_link>
                <link>http://dx.doi.org/10.6019/EMPIAR-10031</link>
            </auxiliary_link>
        </auxiliary_link_list>
    </crossreferences>
    <sample>
        <name>MAVS CARD filament</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>MAVS CARD filament</name>
                <oligomeric_state>filament</oligomeric_state>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="IPS1, KIAA1271, VISA">Mitochondrial antiviral-signaling protein (MAVS), CARD</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.013</theoretical>
                </molecular_weight>
                <oligomeric_state>filament</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
                    <recombinant_cell>HEK293T</recombinant_cell>
                    <recombinant_plasmid>pcDNA3</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">Q7Z434</external_references>
                </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">
                    <concentration units="mg/mL">0.1</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>20 mM Tris-HCl, 50 mM NaCl, 1 mM DTT</details>
                    </buffer>
                    <grid>
                        <details>Quantifoil R2/2 grids coated with thin carbon on top</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <instrument>FEI VITROBOT MARK III</instrument>
                    </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>
                    <nominal_cs units="mm">0.01</nominal_cs>
                    <nominal_defocus_min units="&#181;m">2.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">4.0</nominal_defocus_max>
                    <nominal_magnification>59000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <date>2014-11-05</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">FEI FALCON II (4k x 4k)</film_or_detector_model>
                            <number_real_images>433</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">35</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </helical_microscopy>
            </microscopy_list>
            <helical_processing image_processing_id="1">
                <details>Relion, IHRSR</details>
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">5.06</delta_z>
                            <delta_phi units="deg">101.21</delta_phi>
                            <axial_symmetry>C1</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <resolution res_type="BY AUTHOR" units="&#8491;">4.2</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Relion, IHRSR</name>
                        </software>
                    </software_list>
                    <details>Relion-based IHRSR</details>
                </final_reconstruction>
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="16001">
        <file>emd_6428.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>160</col>
            <row>160</row>
            <sec>160</sec>
        </dimensions>
        <origin>
            <col>48</col>
            <row>48</row>
            <sec>48</sec>
        </origin>
        <spacing>
            <x>160</x>
            <y>160</y>
            <z>160</z>
        </spacing>
        <cell>
            <a units="&#8491;">168.0</a>
            <b units="&#8491;">168.0</b>
            <c units="&#8491;">168.0</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>-0.13635316</minimum>
            <maximum>0.19847907</maximum>
            <average>0.0024924</average>
            <std>0.01761811</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.05</x>
            <y units="&#8491;">1.05</y>
            <z units="&#8491;">1.05</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.04</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Cryo-EM map of MAVS CARD filament</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6428::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3J6J</access_code>
                    <chain>
                        <chain_id>A</chain_id>
                    </chain>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <details>One MAVS CARD molecule was docked into the EM map by rigid body docking. Symmetric copies were generated in Chimera.</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
        <figure_list>
            <figure>
                <file>emd_6428.tif</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>