<?xml version='1.0' encoding='utf-8'?>
<emd emdb_id="EMD-12161" version="3.0.2.4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_2_4/emdb.xsd">
    <admin>
        <current_status>
            <date>2021-03-17</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2020-12-26</deposition>
            <header_release>2021-03-17</header_release>
            <map_release>2021-03-17</map_release>
            <update>2021-03-17</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Swiss National Science Foundation</funding_body>
                <code>NF310030_192644</code>
                <country>Switzerland</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Japan Society for the Promotion of Science (JSPS)</funding_body>
                <code>17H01440</code>
                <country>Japan</country>
            </grant_reference>
        </grant_support>
        <title>Chlamydomonas cilia with MOT7-BCCP labeled</title>
        <authors_list>
            <author>Noga A</author>
            <author>Kutomi O</author>
            <author>Yamamoto R</author>
            <author>Nakagiri Y</author>
            <author>Imai H</author>
            <author>Obbineni JM</author>
            <author>Zimmermann N</author>
            <author>Ishikawa T</author>
            <author>Wakabayashi K</author>
            <author>Kon T</author>
            <author>Inaba K</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Kutomi O</author>
                    <author order="2">Yamamoto R</author>
                    <author order="3">Hirose K</author>
                    <author order="4">Mizuno K</author>
                    <author order="5">Nakagiri Y</author>
                    <author order="6">Imai H</author>
                    <author order="7">Noga A</author>
                    <author order="8">Obbineni JM</author>
                    <author order="9">Zimmermann N</author>
                    <author order="10">Nakajima M</author>
                    <author order="11">Shibata D</author>
                    <author order="12">Shibata M</author>
                    <author order="13">Shiba K</author>
                    <author order="14">Kita M</author>
                    <author order="15">Kigoshi H</author>
                    <author order="16">Tanaka Y</author>
                    <author order="17">Yamasaki Y</author>
                    <author order="18">Asahina Y</author>
                    <author order="19">Song C</author>
                    <author order="20">Nomura M</author>
                    <author order="21">Nomura M</author>
                    <author order="22">Nakajima A</author>
                    <author order="23">Nakachi M</author>
                    <author order="24">Yamada L</author>
                    <author order="25">Nakazawa S</author>
                    <author order="26">Sawada H</author>
                    <author order="27">Murata K</author>
                    <author order="28">Mitsuoka K</author>
                    <author order="29">Ishikawa T</author>
                    <author order="30">Wakabayashi KI</author>
                    <author order="31">Kon T</author>
                    <author order="32">Inaba K</author>
                    <title>A dynein-associated photoreceptor protein prevents ciliary acclimation to blue light.</title>
                    <journal_abbreviation>Sci Adv</journal_abbreviation>
                    <country>US</country>
                    <volume>7</volume>
                    <year>2021</year>
                    <external_references type="PUBMED">33637535</external_references>
                    <external_references type="DOI">doi:10.1126/sciadv.abf3621</external_references>
                    <external_references type="ISSN">2375-2548</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-12160</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>deletion mutant</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-12161</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>doublet microtubules from cilia</name>
        <supramolecule_list>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name>doublet microtubules from cilia</name>
                <parent>0</parent>
                <details>Average of subtomograms extracted from microtubule doublet parts of cilia</details>
                <natural_source database="NCBI">
                    <organism ncbi="3055">Chlamydomonas reinhardtii</organism>
                    <strain>MOT7-BCCP</strain>
                    <organelle>flagella/cilia</organelle>
                    <cellular_location>flagella/cilia</cellular_location>
                </natural_source>
            </organelle_or_cellular_component_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>subtomogramAveraging</method>
            <aggregation_state>filament</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <ph>7.0</ph>
                        <details>TAP medium</details>
                    </buffer>
                    <grid>
                        <model>Quantifoil R3.5/1</model>
                        <material>COPPER</material>
                        <mesh>300</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY ARRAY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>PLASMA CLEANING</type>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <instrument>GATAN CRYOPLUNGE 3</instrument>
                    </vitrification>
                    <details>cilia isolated from the cell and demembraned</details>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_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>
                    <c2_aperture_diameter units="µm">100.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">4.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">5.0</nominal_defocus_max>
                    <nominal_magnification>30000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <basic />
                    </alignment_procedure>
                    <specialist_optics>
                        <energy_filter>
                            <name>GIF Quantum LS</name>
                            <slit_width units="eV">25</slit_width>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <number_grids_imaged>3</number_grids_imaged>
                            <average_exposure_time units="s">1.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">60.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </subtomogram_averaging_microscopy>
            </microscopy_list>
            <subtomogram_averaging_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <resolution res_type="BY AUTHOR" units="Å">25.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                        </software>
                    </software_list>
                    <number_subtomograms_used>2000</number_subtomograms_used>
                </final_reconstruction>
                <extraction>
                    <number_tomograms>20</number_tomograms>
                    <number_images_used>4000</number_images_used>
                </extraction>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                        </software>
                    </software_list>
                </ctf_correction>
                <final_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing />
                </final_angle_assignment>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="17644">
        <file>emd_12161.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>164</col>
            <row>164</row>
            <sec>164</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>-58</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>164</x>
            <y>164</y>
            <z>164</z>
        </spacing>
        <cell>
            <a units="Å">1377.6</a>
            <b units="Å">1377.6</b>
            <c units="Å">1377.6</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>0.0</minimum>
            <maximum>10000.0</maximum>
            <average>3702.3315</average>
            <std>641.7208</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">8.4</x>
            <y units="Å">8.4</y>
            <z units="Å">8.4</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>3900.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-12161::::</label>
        <annotation_details>cilia from Chlamydomonas with MOT7 proteins tagged with BCCP and labeled</annotation_details>
    </map>
</emd>