<emd emdb_id="EMD-3241" 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>2015-11-11</deposition>
            <header_release>2015-11-18</header_release>
            <map_release>2016-03-30</map_release>
            <update>2016-06-15</update>
        </key_dates>
        <title>Cryo-EM reconstruction of caspase-1 CARD</title>
        <authors_list>
            <author>Li Y</author>
            <author>Lu A</author>
            <author>Schmidt FI</author>
            <author>Yin Q</author>
            <author>Chen S</author>
            <author>Fu T-M</author>
            <author>Tong AB</author>
            <author>Ploegh HL</author>
            <author>Mao Y</author>
            <author>Wu H</author>
        </authors_list>
        <keywords>Caspase-1, CARD, inflammasome, filament, cryo-EM, signalosome, helical reconstruction, death domain</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Lu A</author>
                    <author order="2">Li Y</author>
                    <author order="3">Schmidt FI</author>
                    <author order="4">Yin Q</author>
                    <author order="5">Chen S</author>
                    <author order="6">Fu T-M</author>
                    <author order="7">Tong AB</author>
                    <author order="8">Ploegh HL</author>
                    <author order="9">Mao Y</author>
                    <author order="10">Wu H</author>
                    <title>Molecular basis of caspase-1 polymerization and its inhibition by a novel capping mechanism</title>
                    <journal>Nature Structural &amp; Molecular Biology</journal>
                    <volume>23</volume>
                    <first_page>416</first_page>
                    <last_page>425</last_page>
                    <year>2016</year>
                    <external_references type="PUBMED">27043298</external_references>
                    <external_references type="DOI">doi:10.1038/nsmb.3199</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>5fna</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Human caspase-1 CARD</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Human caspase-1 CARD</name>
                <oligomeric_state>helical</oligomeric_state>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Caspase-1 CARD</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                </natural_source>
                <oligomeric_state>Helical</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>BL21 DE3</recombinant_strain>
                    <recombinant_plasmid>pDB-HIs-MBP</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">P29466</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">0.2</concentration>
                    <buffer>
                        <ph>8.0</ph>
                        <details>20 mM Sodium HEPES, pH 8.0, 150 mM NaCl, 2 mM DTT</details>
                    </buffer>
                    <grid>
                        <details>holey carbon C-flat grids (R1.2/1.3, Photochip, CA), glow discharged</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">100</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>blotted for 3 seconds before plunging</method>
                    </vitrification>
                </helical_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <helical_microscopy microscopy_id="1">
                    <microscope>OTHER</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">2.7</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.001</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">0.006</nominal_defocus_max>
                    <calibrated_magnification>28736.0</calibrated_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <date>2015-02-02</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">DIRECT ELECTRON DE-16 (4k x 4k)</film_or_detector_model>
                            <number_real_images>200</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </helical_microscopy>
            </microscopy_list>
            <helical_processing image_processing_id="1">
                <details>The particles were aligned using IHRSR</details>
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">5.1</delta_z>
                            <delta_phi units="deg">100.2</delta_phi>
                            <axial_symmetry>C1</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">4.8</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>SPIDER, IHRSR</name>
                        </software>
                    </software_list>
                </final_reconstruction>
                <ctf_correction>
                    <details>Each micrograph</details>
                </ctf_correction>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="16001">
        <file>emd_3241.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>-80</col>
            <row>-80</row>
            <sec>-79</sec>
        </origin>
        <spacing>
            <x>160</x>
            <y>160</y>
            <z>160</z>
        </spacing>
        <cell>
            <a units="&#8491;">139.2</a>
            <b units="&#8491;">139.2</b>
            <c units="&#8491;">139.2</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>-2.27765226</minimum>
            <maximum>5.90264797</maximum>
            <average>0.71799731</average>
            <std>0.87744838</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">0.87</x>
            <y units="&#8491;">0.87</y>
            <z units="&#8491;">0.87</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>3.15</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of caspase-1 CARD filament</annotation_details>
        <details>::::EMDATABANK.org::::EMD-3241::::</details>
    </map>
</emd>