<emd emdb_id="EMD-2079" 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>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2012-04-19</deposition>
            <header_release>2012-07-09</header_release>
            <map_release>2012-11-21</map_release>
            <update>2013-01-09</update>
        </key_dates>
        <title>Electron cryo-microscopy of microtubule-bound human kinesin-5 motor domain in rigor state (gold cluster in loop5 T126C).</title>
        <authors_list>
            <author>Goulet A</author>
            <author>Behnke-Parks WM</author>
            <author>Sindelar CV</author>
            <author>Major J</author>
            <author>Rosenfeld SS</author>
            <author>Moores CA</author>
        </authors_list>
        <keywords>electron cryo-microscopy, kinesin, microtubule, mitosis, cancer</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Goulet A</author>
                    <author order="2">Behnke-Parks WM</author>
                    <author order="3">Sindelar CV</author>
                    <author order="4">Major J</author>
                    <author order="5">Rosenfeld SS</author>
                    <author order="6">Moores CA</author>
                    <title>The structural basis of force generation by the mitotic motor kinesin-5.</title>
                    <journal>J.BIOL.CHEM.</journal>
                    <volume>287</volume>
                    <first_page>44654</first_page>
                    <last_page>44666</last_page>
                    <year>2012</year>
                    <external_references type="PUBMED">23135273</external_references>
                    <external_references type="DOI">doi:10.1074/jbc.M112.404228</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>13-protofilament microtubule-bound human kinesin-5 motor domain in absence of nucleotides. A gold cluster is attached to loop5 (T126C).</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>13-protofilament microtubule-bound human kinesin-5 motor domain in absence of nucleotides. A gold cluster is attached to loop5 (T126C).</name>
                <oligomeric_state>13-protofilament microtubule with one kinesin-5 motor domain bound every tubulin heterodimers</oligomeric_state>
                <number_unique_components>3</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="TUBULIN ALPHA-1D CHAIN">alpha tubulin</name>
                <natural_source database="NCBI">
                    <organism ncbi="9913">Bos taurus</organism>
                    <synonym_organism>Cattle</synonym_organism>
                    <tissue>brain</tissue>
                </natural_source>
                <oligomeric_state>heterodimer</oligomeric_state>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence>
                    <external_references type="INTERPRO">IPR002452</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name synonym="TUBULIN BETA-2B CHAIN">beta tubulin</name>
                <natural_source database="NCBI">
                    <organism ncbi="9913">Bos taurus</organism>
                    <tissue>brain</tissue>
                </natural_source>
                <oligomeric_state>heterodimer</oligomeric_state>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence>
                    <external_references type="INTERPRO">IPR013838</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name synonym="KINESIN-LIKE PROTEIN KIF11">Kinesin-5 motor domain</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                </natural_source>
                <details>undecagold cluster was attached to the specific cysteine residue in loop5 (T126C)</details>
                <oligomeric_state>monomer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_plasmid>pET21a</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="INTERPRO">IPR019821</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">
                    <buffer>
                        <ph>6.8</ph>
                        <details>80 mM PIPES, 5 mM MgCl2, 1 mM EGTA, 1 U/mL apyrase</details>
                    </buffer>
                    <grid>
                        <details>400 mesh holey carbon grids</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <instrument>FEI VITROBOT MARK I</instrument>
                        <method>chamber at 24 degrees C, blot 2.5 sec</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F20</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">2.0</nominal_cs>
                    <nominal_defocus_min units="&#181;m">1.2</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.4</nominal_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">90</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 150,000 times magnification</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2011-11-09</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>ZEISS SCAI</scanner>
                                <sampling_interval units="&#181;m">7</sampling_interval>
                            </digitization_details>
                            <number_real_images>30</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">18</average_electron_dose_per_image>
                            <bits_per_pixel>8.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>The particles were selected along individual microtubules.</details>
                <ctf_correction>
                    <details>FREALIGN</details>
                </ctf_correction>
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">11.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>SPIDER, FREALIGN</name>
                        </software>
                    </software_list>
                    <details>Approximately 23,000 asymmetric units were averaged in the final reconstruction.
The deposited map is low pass filtered at 16 A.</details>
                    <number_images_used>2027</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="357">
        <file>emd_2079.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>45</col>
            <row>45</row>
            <sec>45</sec>
        </dimensions>
        <origin>
            <col>-28</col>
            <row>-14</row>
            <sec>-42</sec>
        </origin>
        <spacing>
            <x>45</x>
            <y>45</y>
            <z>45</z>
        </spacing>
        <cell>
            <a units="&#8491;">126.0</a>
            <b units="&#8491;">126.0</b>
            <c units="&#8491;">126.0</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>-6.72172165</minimum>
            <maximum>7.19623137</maximum>
            <average>0.23717062</average>
            <std>1.92618001</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.8</x>
            <y units="&#8491;">2.8</y>
            <z units="&#8491;">2.8</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.37</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>3D reconstruction of microtubule-bound human kinesin-5 motor domain with an empty nucleotide-binding site and a gold cluster attached to loop5 (T126C).</annotation_details>
        <details>::::EMDATABANK.org::::EMD-2079::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_2079.jpg</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>