<?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_9_2/emdb.xsd" version="3.0.9.2" emdb_id="EMD-0438">
    <admin>
        <current_status>
            <date>2024-03-20</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2018-12-12</deposition>
            <header_release>2019-01-23</header_release>
            <map_release>2019-01-23</map_release>
            <update>2024-03-20</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)</funding_body>
                <code>Al124491</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health &amp; Human Development (NIH/NICHD)</funding_body>
                <code>HD087988</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Cryo-EM structure of NLRP6 PYD filament</title>
        <authors_list>
            <author>Shen C</author>
            <author>Fu TM</author>
            <author>Wu H</author>
        </authors_list>
        <keywords>death domain fold, helical assembly, inflammasome, SIGNALING PROTEIN, PROTEIN FIBRIL</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Shen C</author>
                    <author order="2">Lu A</author>
                    <author order="3">Xie WJ</author>
                    <author order="4">Ruan J</author>
                    <author order="5">Negro R</author>
                    <author order="6">Egelman EH</author>
                    <author order="7">Fu TM</author>
                    <author order="8">Wu H</author>
                    <title>Molecular mechanism for NLRP6 inflammasome assembly and activation.</title>
                    <journal_abbreviation>Proc. Natl. Acad. Sci. U.S.A.</journal_abbreviation>
                    <country>US</country>
                    <volume>116</volume>
                    <first_page>2052</first_page>
                    <last_page>2057</last_page>
                    <year>2019</year>
                    <external_references type="PUBMED">30674671</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1817221116</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>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6ncv</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>NLRP6 PYD</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>NLRP6 PYD</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>NACHT, LRR and PYD domains-containing protein 6</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.011931579</theoretical>
                </molecular_weight>
                <number_of_copies>21</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="7108">Spodoptera frugiperda</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MDQPEAPCSSTGPRLAVARELLLAALEELSQEQLKRFRHKLRDVGPDGRSIPWGRLERADAVDLAEQLAQFYGPEPALEV
ARKTLKRADARDVAAQLQERRLQRLG</string>
                    <external_references type="UNIPROTKB">P59044</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">1.5</concentration>
                    <buffer>
                        <ph>7.4</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 K2 SUMMIT (4k 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">13.8</delta_z>
                            <delta_phi units="deg">56.8</delta_phi>
                            <axial_symmetry>C3</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">3.7</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <number_images_used>181477</number_images_used>
                </final_reconstruction>
                <startup_model type_of_model="PDB ENTRY">
                    <pdb_model>
                        <pdb_id>3J63</pdb_id>
                    </pdb_model>
                </startup_model>
                <final_angle_assignment>
                    <type>NOT APPLICABLE</type>
                </final_angle_assignment>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="23329">
        <file>emd_0438.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>180</col>
            <row>180</row>
            <sec>180</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>180</x>
            <y>180</y>
            <z>180</z>
        </spacing>
        <cell>
            <a units="Å">190.79999</a>
            <b units="Å">190.79999</b>
            <c units="Å">190.79999</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>-0.15548103</minimum>
            <maximum>0.32674178</maximum>
            <average>0.0038273952</average>
            <std>0.01951139</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.06</x>
            <y units="Å">1.06</y>
            <z units="Å">1.06</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.1</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-0438::::</label>
        <annotation_details>NLRP6 PYD filament</annotation_details>
    </map>
</emd>
