<emd emdb_id="EMD-5330" 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>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2011-08-10</deposition>
            <header_release>2011-08-11</header_release>
            <map_release>2012-06-21</map_release>
            <update>2014-04-02</update>
        </key_dates>
        <title>Cryo-electron tomography reveals novel interactions and doublet-specific structures in the I1 dynein</title>
        <authors_list>
            <author>Heuser T</author>
            <author>Barber CF</author>
            <author>Lin J</author>
            <author>Krell J</author>
            <author>Rebesco M</author>
            <author>Porter ME</author>
            <author>Nicastro D</author>
        </authors_list>
        <keywords>axoneme,molecular motor,motility regulation,flagella</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Heuser T</author>
                    <author order="2">Barber CF</author>
                    <author order="3">Lin J</author>
                    <author order="4">Krell J</author>
                    <author order="5">Rebesco M</author>
                    <author order="6">Porter ME</author>
                    <author order="7">Nicastro D</author>
                    <title>Cryoelectron tomography reveals doublet-specific structures and unique interactions in the I1 dynein.</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <volume>109</volume>
                    <first_page>e2067</first_page>
                    <last_page>e2076</last_page>
                    <year>2012</year>
                    <external_references type="PUBMED">22733763</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1120690109</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Cryo-electron tomography and subtomographic average (750 axonemal repeats) of isolated axonemes of wild type Chlamydomonas (CC 125, 137c), I1 dynein complex (dynein f) is bound to the doublet microtubule and is connected to neighboring structures.</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Cryo-electron tomography and subtomographic average (750 axonemal repeats) of isolated axonemes of wild type Chlamydomonas (CC 125, 137c), I1 dynein complex (dynein f) is bound to the doublet microtubule and is connected to neighboring structures.</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name synonym="dynein f">I1 dynein complex</name>
                <number_of_copies>2</number_of_copies>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <natural_source database="NCBI">
                    <organism ncbi="3055">Chlamydomonas reinhardtii</organism>
                    <strain>CC-125, 137c</strain>
                    <synonym_organism>unicellular green algae</synonym_organism>
                    <cell>Chlamydomonas reinhardtii</cell>
                    <organelle>eukaryotic flagella</organelle>
                </natural_source>
                <recombinant_expression database="NCBI" />
            </organelle_or_cellular_component_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>subtomogramAveraging</method>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <concentration units="mg/mL">1</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <details>10 mM HEPES, pH 7.4, 25 mM NaCl, 4 mM MgSO4, 1 mM EGTA, 0.1 mM EDTA</details>
                    </buffer>
                    <grid>
                        <details>Quantifoil holey carbon grids Cu 200 mesh R2/2</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_temperature units="K">100</chamber_temperature>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <method>front-side blotting for 2-3 seconds</method>
                    </vitrification>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F30</microscope>
                    <illumination_mode>OTHER</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <nominal_defocus_min units="&#181;m">6.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">8.0</nominal_defocus_max>
                    <nominal_magnification>13500.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">80</temperature_average>
                    </temperature>
                    <specialist_optics>
                        <energy_filter>
                            <name>GATAN postcolumn filter GIF</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>2004-02-20</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GENERIC GATAN (2k x 2k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">100</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Eucentric</specimen_holder>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">-60</min_angle>
                            <max_angle units="deg">60</max_angle>
                        </axis1>
                    </tilt_series>
                </subtomogram_averaging_microscopy>
            </microscopy_list>
            <subtomogram_averaging_processing image_processing_id="1">
                <details>750 axonemal repeats (96 nm long) from 5 tomograms (reconstructed using fiducial alignment and weighted backprojection, IMOD software, Kremer et al. 1996) were aligned and averaged using the PEET software (bio3d.colorado.edu, Nicastro et al. 2006). Average number of tilts used in the 3D reconstructions: 80. Average tomographic tilt angle increment: 1.5.</details>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">39.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                        </software>
                    </software_list>
                    <details>Final maps were calculated by averaging 750 particles from 5 tomograms</details>
                </final_reconstruction>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="345">
        <file>emd_5330.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>55</col>
            <row>40</row>
            <sec>40</sec>
        </dimensions>
        <origin>
            <col>-21</col>
            <row>-53</row>
            <sec>-64</sec>
        </origin>
        <spacing>
            <x>55</x>
            <y>40</y>
            <z>40</z>
        </spacing>
        <cell>
            <a units="&#8491;">380.0</a>
            <b units="&#8491;">522.5</b>
            <c units="&#8491;">380.0</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>109.595199579999999</minimum>
            <maximum>148.880630489999987</maximum>
            <average>124.201629639999993</average>
            <std>5.68234873</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">9.5</x>
            <y units="&#8491;">9.5</y>
            <z units="&#8491;">9.5</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>127.5</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>This is a subtomogram average of the I1 inner dynein complex in wild type Chlamydomonas flagella</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5330::::</details>
    </map>
</emd>