<emd emdb_id="EMD-6051" 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>2014-08-26</deposition>
            <header_release>2014-09-24</header_release>
            <map_release>2014-11-05</map_release>
            <update>2014-12-17</update>
        </key_dates>
        <title>Cryo-EM structure of the yeast dynein motor domain in the presence of ADP-vanadate</title>
        <authors_list>
            <author>Bhabha G</author>
            <author>Moeller A</author>
            <author>Liao M</author>
            <author>Speir JA</author>
            <author>Vale RD</author>
            <author>Cheng Y</author>
        </authors_list>
        <keywords>motor proteins, power stroke, dynein, AAA protein, ATPase</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Bhabha G</author>
                    <author order="2">Cheng HC</author>
                    <author order="3">Zhang N</author>
                    <author order="4">Moeller A</author>
                    <author order="5">Liao M</author>
                    <author order="6">Speir JA</author>
                    <author order="7">Cheng Y</author>
                    <author order="8">Vale RD</author>
                    <title>Allosteric Communication in the Dynein Motor Domain.</title>
                    <journal>CELL(CAMBRIDGE,MASS.)</journal>
                    <volume>159</volume>
                    <first_page>857</first_page>
                    <last_page>868</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">25417161</external_references>
                    <external_references type="DOI">doi:10.1016/j.cell.2014.10.018</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>yeast dynein motor domain in the presence of ADP-vanadate</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>yeast dynein motor domain in the presence of ADP-vanadate</name>
                <oligomeric_state>monomer</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">0.303</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>dynein</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                    <strain>VY1027</strain>
                    <synonym_organism>yeast</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.303</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <oligomeric_state>monomer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="4932">Saccharomyces cerevisiae</recombinant_organism>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">P36022</external_references>
                </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">0.2</concentration>
                    <buffer>
                        <ph>8.0</ph>
                        <details>50 mM Tris, pH 8.0, 200 mM sodium chloride, 1 mM EGTA, 2 mM magnesium acetate, 1 mM DTT</details>
                    </buffer>
                    <grid>
                        <details>Quantifoil, Cu 400 mesh, R1.2/1.3</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <instrument>FEI VITROBOT MARK II</instrument>
                        <method>blot for 4 seconds before plunging</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI POLARA 300</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">2.0</nominal_cs>
                    <nominal_defocus_min units="&#181;m">1.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.5</nominal_defocus_max>
                    <nominal_magnification>31000.0</nominal_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <details>Gatan K2 Summit operated in super-resolution counting mode; image recorded with dose fractionation method.</details>
                    <date>2013-11-03</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN K2 (4k x 4k)</film_or_detector_model>
                            <number_real_images>657</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">21</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>cooled to liquid nitrogen temperature</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">14.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Relion</name>
                        </software>
                    </software_list>
                    <number_images_used>5127</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="932">
        <file>emd_6051.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>62</col>
            <row>62</row>
            <sec>62</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>62</x>
            <y>62</y>
            <z>62</z>
        </spacing>
        <cell>
            <a units="&#8491;">225.68001</a>
            <b units="&#8491;">225.68001</b>
            <c units="&#8491;">225.68001</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>-0.0858372</minimum>
            <maximum>0.1577021</maximum>
            <average>0.00290975</average>
            <std>0.0161445</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">3.64</x>
            <y units="&#8491;">3.64</y>
            <z units="&#8491;">3.64</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.044</level>
                <source>EMDB</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of yeast dynein motor domain in the presence of 5 mM ADP-vanadate (prepared by mixing ATP and sodium vanadate at equimolar concentrations)</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6051::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_6051.png</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>