<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_5/emdb.xsd" emdb_id="EMD-4509" version="3.0.1.5">
    <admin>
        <current_status>
            <date>2019-09-11</date>
            <code>OBS</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2018-12-28</deposition>
            <header_release>2019-08-21</header_release>
            <map_release>2019-08-21</map_release>
            <obsolete>2019-09-11</obsolete>
            <update>2019-09-11</update>
        </key_dates>
        <superseded_by_list>
            <entry>
                <date>2019-09-11</date>
                <entry>EMD-4510</entry>
            </entry>
        </superseded_by_list>
        <title>Cryo em structure of the Listeria stressosome</title>
        <authors_list>
            <author>Williams AH</author>
            <author>Redzej A</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Williams AH</author>
                    <author order="2">Redzej A</author>
                    <author order="3">Rolhion N</author>
                    <author order="4">Costa TRD</author>
                    <author order="5">Rifflet A</author>
                    <author order="6">Waksman G</author>
                    <author order="7">Cossart P</author>
                    <title>The cryo-electron microscopy supramolecular structure of the bacterial stressosome unveils its mechanism of activation.</title>
                    <journal_abbreviation>Nat Commun</journal_abbreviation>
                    <country>UK</country>
                    <volume>10</volume>
                    <first_page>3005</first_page>
                    <last_page>3005</last_page>
                    <year>2019</year>
                    <external_references type="PUBMED">31285450</external_references>
                    <external_references type="DOI">doi:10.1038/s41467-019-10782-0</external_references>
                    <external_references type="ISSN">2041-1723</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-4508</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-4509</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Listeria Stressosome</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Listeria Stressosome</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>
                <details>The subcomponents are, RsbR, RsbR and he RsbT.</details>
                <natural_source database="NCBI">
                    <organism ncbi="1639">Listeria monocytogenes</organism>
                    <strain>EGD-e</strain>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>Bl21</recombinant_strain>
                </recombinant_expression>
                <molecular_weight>
                    <experimental units="MDa">1.8</experimental>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>RsbR</name>
                <natural_source database="NCBI">
                    <organism ncbi="1639">Listeria monocytogenes</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="511693">Escherichia coli BL21</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MYKDFANFIRTNKADLLNDWMNEMEKQSDQLINDIAKEAMYEETSKEFVDLIVSNVTENGSKFNEKLDDF
AEKVVHLGWPIHFVTTGLRVFGLLVYTAMRDEDLFLKREEKPEDDAYYRFETWLSSMYNKVVTAYADTWE
KTVSIQKSALQELSAPLLPIFEKISVMPLIGTIDTERAKLIIENLLIGVVKNRSEVVLIDITGVPVVDTM
VAHHIIQASEAVRLVGCQAMLVGIRPEIAQTIVNLGIELDQIITTNTMKKGMERALALTNREIVEKEG

</string>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>RsbS</name>
                <natural_source database="NCBI">
                    <organism ncbi="1639">Listeria monocytogenes</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="511693">Escherichia coli BL21</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MGIPILKLGECLLISIQSELDDHTAVEFQEDLLAKIHETSARGVVIDITSIDFIDSFIAKILGDVVSMSK
LMGAKVVVTGIQPAVAITLIELGITFSGVLSAMDLESGLEKLKQELGE</string>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name>RsbT</name>
                <natural_source database="NCBI">
                    <organism ncbi="1639">Listeria monocytogenes</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="511693">Escherichia coli BL21</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MTFQSCVKIINEWDIVAARQLGRKISKEIGFGTVDQARITTAISELARNIFLYAGRGEICIEKVSESGKQ
GMIIVAKDKGPGIVDIRKVMQDGYTTSGGLGAGLPGVKRLMDSFDIESSIEGDSKGTVITTTKWVR
</string>
                </sequence>
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>singleParticle</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <concentration units="mg/mL">0.02</concentration>
                    <buffer>
                        <ph>8.5</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE-PROPANE</cryogen_name>
                        <details></details>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</microscope>
                    <illumination_mode>OTHER</illumination_mode>
                    <imaging_mode>OTHER</imaging_mode>
                    <electron_source>OTHER</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 QUANTUM (4k x 4k)</film_or_detector_model>
                            <detector_mode>SUPER-RESOLUTION</detector_mode>
                            <average_exposure_time units="s">10.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">2.25</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <particle_selection>
                    <number_selected>100000</number_selected>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>CTFFIND</name>
                        </software>
                    </software_list>
                </ctf_correction>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C2</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">4.4</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                    <number_images_used>78000</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>OTHER</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>ANGULAR RECONSTITUTION</type>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="275685">
        <file>emd_4509.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>410</col>
            <row>410</row>
            <sec>410</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>410</x>
            <y>410</y>
            <z>410</z>
        </spacing>
        <cell>
            <a units="Å">168100.0</a>
            <b units="Å">168100.0</b>
            <c units="Å">168100.0</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>-0.045431003</minimum>
            <maximum>0.0974124</maximum>
            <average>0.0004691323</average>
            <std>0.003942631</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">410.0</x>
            <y units="Å">410.0</y>
            <z units="Å">410.0</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0152</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-4509::::</label>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>OTHER</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
