<emd emdb_id="EMD-6102" 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>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2014-09-21</deposition>
            <header_release>2015-01-21</header_release>
            <map_release>2015-05-27</map_release>
            <update>2015-06-03</update>
        </key_dates>
        <title>Electron cryo-microscopy of DNGR-1 in complex with F-actin</title>
        <authors_list>
            <author>Hanc P</author>
            <author>Fujii T</author>
            <author>Yamada Y</author>
            <author>Huotari J</author>
            <author>Schulz O</author>
            <author>Ahrens S</author>
            <author>Kjaer S</author>
            <author>Way M</author>
            <author>Namba K</author>
            <author>Reis e Sousa C</author>
        </authors_list>
        <keywords>DNGR-1, Actin, Damage-associated molecular patterns</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Hanc P</author>
                    <author order="2">Fujii T</author>
                    <author order="3">Iborra S</author>
                    <author order="4">Yamada Y</author>
                    <author order="5">Huotari J</author>
                    <author order="6">Schulz O</author>
                    <author order="7">Ahrens S</author>
                    <author order="8">Kjaer S</author>
                    <author order="9">Way M</author>
                    <author order="10">Sancho D</author>
                    <author order="11">Namba K</author>
                    <author order="12">Reis e Sousa C</author>
                    <title>Structure of the Complex of F-Actin and DNGR-1, a C-Type Lectin Receptor Involved in Dendritic Cell Cross-Presentation of Dead Cell-Associated Antigens</title>
                    <journal>IMMUNITY</journal>
                    <volume>42</volume>
                    <first_page>839</first_page>
                    <last_page>849</last_page>
                    <year>2015</year>
                    <external_references type="PUBMED">25979418</external_references>
                    <external_references type="DOI">doi:10.1016/j.immuni.2015.04.009</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3j82</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>F-actin complexed with mouse DNGR-1 extracellular domain</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>F-actin complexed with mouse DNGR-1 extracellular domain</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="CLEC9A">DNGR-1</name>
                <natural_source database="NCBI">
                    <organism ncbi="10090">Mus musculus</organism>
                    <synonym_organism>Mouse</synonym_organism>
                </natural_source>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <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">
                    <buffer>
                        <ph>7.5</ph>
                        <details>25mM Hepes buffer (pH 7.5), 100mM KCl, 1mM MgCl2, 1mM ATP</details>
                    </buffer>
                    <grid>
                        <details>R0.6/1.0, Quantifoil</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <instrument>FEI VITROBOT MARK II</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 3200FSC</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">1.6</nominal_cs>
                    <nominal_defocus_min units="&#181;m">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.0</nominal_defocus_max>
                    <nominal_magnification>60000.0</nominal_magnification>
                    <calibrated_magnification>109489.0</calibrated_magnification>
                    <specimen_holder_model>JEOL 3200FSC CRYOHOLDER</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">50</temperature_min>
                        <temperature_max units="K">60</temperature_max>
                        <temperature_average units="K">55</temperature_average>
                    </temperature>
                    <specialist_optics>
                        <energy_filter>
                            <name>JEOL Omega filter</name>
                            <lower_energy_threshold units="eV">0.0</lower_energy_threshold>
                            <upper_energy_threshold units="eV">20.0</upper_energy_threshold>
                        </energy_filter>
                    </specialist_optics>
                    <date>2012-12-10</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">TVIPS TEMCAM-F416 (4k x 4k)</film_or_detector_model>
                            <number_real_images>774</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>Each Particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">7.7</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Spider, EMAN</name>
                        </software>
                    </software_list>
                    <number_images_used>73608</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="3908">
        <file>emd_6102.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>100</sec>
        </dimensions>
        <origin>
            <col>-50</col>
            <row>-50</row>
            <sec>-50</sec>
        </origin>
        <spacing>
            <x>100</x>
            <y>100</y>
            <z>100</z>
        </spacing>
        <cell>
            <a units="&#8491;">137.0</a>
            <b units="&#8491;">137.0</b>
            <c units="&#8491;">137.0</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>-4.13731623</minimum>
            <maximum>5.36457253</maximum>
            <average>0.15745416</average>
            <std>0.67706984</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.37</x>
            <y units="&#8491;">1.37</y>
            <z units="&#8491;">1.37</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.838</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of DNGR1 in complex with F-actin</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6102::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3J82</access_code>
                    <chain>
                        <chain_id>A</chain_id>
                    </chain>
                    <chain>
                        <chain_id>B</chain_id>
                    </chain>
                    <chain>
                        <chain_id>C</chain_id>
                    </chain>
                    <chain>
                        <chain_id>D</chain_id>
                    </chain>
                </initial_model>
                <software_list>
                    <software>
                        <name>Spider, EMAN</name>
                    </software>
                </software_list>
                <details>Single particle--Applied symmetry: C1</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>