<?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_3/emdb.xsd" version="3.0.9.3" emdb_id="EMD-10500">
    <admin>
        <current_status>
            <date>2024-05-22</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-11-17</deposition>
            <header_release>2020-01-29</header_release>
            <map_release>2020-02-19</map_release>
            <update>2024-05-22</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>European Commission</funding_body>
                <code>PIEF-GA-2012-331285</code>
                <country>Germany</country>
            </grant_reference>
            <grant_reference>
                <funding_body>European Commission</funding_body>
                <code>PCOFUND-GA-2008-229597</code>
                <country>Germany</country>
            </grant_reference>
            <grant_reference>
                <funding_body>German Research Foundation</funding_body>
                <code>EXC1074</code>
                <country>Germany</country>
            </grant_reference>
        </grant_support>
        <title>Cryo-EM structure of AtNBR1-PB1 filament (S-type)</title>
        <authors_list>
            <author>Jakobi AJ</author>
            <author>Sachse C</author>
        </authors_list>
        <keywords>Autophagy, helical filament, SIGNALING PROTEIN</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0002-7761-2027" order="1">Jakobi AJ</author>
                    <author ORCID="0000-0003-3721-5104" order="2">Huber ST</author>
                    <author order="3">Mortensen SA</author>
                    <author order="4">Schultz SW</author>
                    <author order="5">Palara A</author>
                    <author order="6">Kuhm T</author>
                    <author order="7">Shrestha BK</author>
                    <author ORCID="0000-0001-6338-3342" order="8">Lamark T</author>
                    <author order="9">Hagen WJH</author>
                    <author ORCID="0000-0002-4643-5435" order="10">Wilmanns M</author>
                    <author ORCID="0000-0003-1451-9578" order="11">Johansen T</author>
                    <author order="12">Brech A</author>
                    <author ORCID="0000-0002-1168-5143" order="13">Sachse C</author>
                    <title>Structural basis of p62/SQSTM1 helical filaments and their role in cellular cargo uptake.</title>
                    <journal_abbreviation>Nat Commun</journal_abbreviation>
                    <country>UK</country>
                    <volume>11</volume>
                    <first_page>440</first_page>
                    <last_page>440</last_page>
                    <year>2020</year>
                    <external_references type="PUBMED">31974402</external_references>
                    <external_references type="DOI">doi:10.1038/s41467-020-14343-8</external_references>
                    <external_references type="ISSN">2041-1723</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6tgp</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>AtNBR1-PB1 (S-type)</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>AtNBR1-PB1 (S-type)</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <details>Helical filament of AtNBR1-PB1 domain (1-95)</details>
                <natural_source database="NCBI">
                    <organism ncbi="3702">Arabidopsis thaliana</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Protein NBR1 homolog</name>
                <natural_source database="NCBI">
                    <organism ncbi="3702">Arabidopsis thaliana</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.010198557</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="469008">Escherichia coli BL21(DE3)</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MESTANALVVKVSYGGVLRRFRVPVKANGQLDLEMAGLKEKIAALFNLSADAELSLTYSDEDGDVVALVDDNDLFDVTNQ
RLKFLKINVNAGVS</string>
                    <external_references type="UNIPROTKB">Q9SB64</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">0.4</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <component>
                            <concentration units="mM">50.0</concentration>
                            <name>HEPES</name>
                        </component>
                        <component>
                            <concentration units="mM">150.0</concentration>
                            <formula>NaCl</formula>
                            <name>Sodium chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">0.05</concentration>
                            <name>TCEP</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>C-flat-1.2/1.3 4C</model>
                        <material>COPPER</material>
                        <mesh>400</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <time units="s">60</time>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">288</chamber_temperature>
                        <instrument>LEICA EM GP</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">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">0.5</nominal_defocus_min>
                    <nominal_defocus_max units="µm">4.5</nominal_defocus_max>
                    <nominal_magnification>59000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <coma_free/>
                    </alignment_procedure>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI FALCON II (4k x 4k)</film_or_detector_model>
                            <detector_mode>INTEGRATING</detector_mode>
                            <number_real_images>684</number_real_images>
                            <average_electron_dose_per_image units="e/Å^2">14.0</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">5.905</delta_z>
                            <delta_phi units="deg">-31.17</delta_phi>
                            <axial_symmetry>C1</axial_symmetry>
                        </helical_parameters>
                    </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>SPRING</name>
                            <version>0.85</version>
                        </software>
                    </software_list>
                    <number_images_used>18021</number_images_used>
                </final_reconstruction>
                <startup_model type_of_model="NONE"/>
                <final_angle_assignment>
                    <type>NOT APPLICABLE</type>
                    <software_list>
                        <software>
                            <name>SPRING</name>
                            <version>0.85</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="5601">
        <file>emd_10500.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>100</col>
            <row>100</row>
            <sec>140</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>100</x>
            <y>100</y>
            <z>140</z>
        </spacing>
        <cell>
            <a units="Å">138.6</a>
            <b units="Å">138.6</b>
            <c units="Å">194.04001</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>-2.8809712</minimum>
            <maximum>3.9452217</maximum>
            <average>0.000000001985075</average>
            <std>0.99999964</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.386</x>
            <y units="Å">1.386</y>
            <z units="Å">1.386</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.1</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-10500::::</label>
        <annotation_details>Globally sharpened map</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
                <target_criteria>Correlation coefficient</target_criteria>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
