<emd emdb_id="EMD-6393" 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>2015-07-18</deposition>
            <header_release>2015-09-23</header_release>
            <map_release>2015-09-23</map_release>
            <update>2015-10-07</update>
        </key_dates>
        <title>Structural basis for TBC-DEG assembly with TBCC and soluble tubulin dimer</title>
        <authors_list>
            <author>Nithianantham S</author>
            <author>Le S</author>
            <author>Seto E</author>
            <author>Jia W</author>
            <author>Leary J</author>
            <author>Corbett KD</author>
            <author>Moore JK</author>
            <author>Al-Bassam J</author>
        </authors_list>
        <keywords>Tubulin cofactors, Microtubule dynamics, Chaperones, tubulin biogenesis or degradation, tubulin dimer, TBC-DEG, TBCC</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Nithianantham S</author>
                    <author order="2">Le S</author>
                    <author order="3">Seto E</author>
                    <author order="4">Jia W</author>
                    <author order="5">Leary J</author>
                    <author order="6">Corbett KD</author>
                    <author order="7">Moore JK</author>
                    <author order="8">Al-Bassam J</author>
                    <title>Tubulin cofactors and Arl2 are cage-like chaperones that regulate the soluble alphabeta-tubulin pool for microtubule dynamics.</title>
                    <journal>eLife</journal>
                    <volume>4</volume>
                    <year>2015</year>
                    <external_references type="PUBMED">26208336</external_references>
                    <external_references type="DOI">doi:10.7554/eLife.08811</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <auxiliary_link_list>
            <auxiliary_link>
                <link>http://dx.doi.org/10.6019/EMPIAR-10034</link>
            </auxiliary_link>
        </auxiliary_link_list>
    </crossreferences>
    <sample>
        <name>Tubulin cofactor complex (TBC-DEG) with TBCC and tubulin dimer</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Tubulin cofactor complex (TBC-DEG) with TBCC and tubulin dimer</name>
                <details>TBC-DEG:TBCC:tubulin complex behaves as a single biochemical entity.</details>
                <oligomeric_state>One heterotrimer of TBC-DEG binds to TBCC and tubulin dimer</oligomeric_state>
                <number_unique_components>6</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.340</experimental>
                    <theoretical units="MDa">0.345</theoretical>
                    <method>SEC-MALS</method>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="TBCD">tubulin folding cofactor D</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                    <synonym_organism>Baker's yeast</synonym_organism>
                </natural_source>
                <number_of_copies>1</number_of_copies>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_plasmid>pDEST</recombinant_plasmid>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name synonym="TBCE">tubulin folding cofactor E</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                    <synonym_organism>Baker's yeast</synonym_organism>
                </natural_source>
                <number_of_copies>1</number_of_copies>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_plasmid>pDEST</recombinant_plasmid>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name synonym="DEG(Q73L)">ARL2 GTPase, Q73L mutant</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                    <synonym_organism>Baker's yeast</synonym_organism>
                </natural_source>
                <details>Arl2 locked mutant (Q73L) in a GTP-like state</details>
                <number_of_copies>1</number_of_copies>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_plasmid>pDEST</recombinant_plasmid>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="4">
                <name synonym="TBCC">tubulin binding cofactor C</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                    <synonym_organism>Baker's yeast</synonym_organism>
                </natural_source>
                <number_of_copies>1</number_of_copies>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_plasmid>pDEST</recombinant_plasmid>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="5">
                <name>alpha tubulin</name>
                <natural_source database="NCBI">
                    <organism ncbi="32644">unidentified</organism>
                </natural_source>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="6">
                <name>beta tubulin</name>
                <natural_source database="NCBI">
                    <organism ncbi="32644">unidentified</organism>
                </natural_source>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <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">0.5</concentration>
                    <buffer>
                        <ph>7.0</ph>
                        <details>50 mM HEPES, 100 mM KCl, 0.1 mM GTP, 3 mM b-mercaptoethanol</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>The proteins were incubated on carbon-coated grids, briefly washed, and stained with 1% uranyl formate.</details>
                    </staining>
                    <grid>
                        <details>glow-discharged 200 mesh gold grid with thin carbon support</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>NONE</cryogen_name>
                        <instrument>OTHER</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 2100F</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_defocus_min units="&#181;m">1.1</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.7</nominal_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <calibrated_magnification>50050.0</calibrated_magnification>
                    <specimen_holder_model>JEOL</specimen_holder_model>
                    <date>2014-07-25</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>PRIMESCAN</scanner>
                                <sampling_interval units="&#181;m">3.7</sampling_interval>
                            </digitization_details>
                            <number_real_images>100</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">9</average_electron_dose_per_image>
                            <bits_per_pixel>5.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>TBC-DEG:TBCC:tubulin complex particles were picked semi-automatically using e2boxer.py.</details>
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">24.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Spider, EMAN2</name>
                        </software>
                    </software_list>
                    <number_images_used>19500</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>400</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="8193">
        <file>emd_6393.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>128</col>
            <row>128</row>
            <sec>128</sec>
        </dimensions>
        <origin>
            <col>-64</col>
            <row>-64</row>
            <sec>-64</sec>
        </origin>
        <spacing>
            <x>128</x>
            <y>128</y>
            <z>128</z>
        </spacing>
        <cell>
            <a units="&#8491;">256.0</a>
            <b units="&#8491;">256.0</b>
            <c units="&#8491;">256.0</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>-0.00000127</minimum>
            <maximum>0.08629292</maximum>
            <average>0.00090515</average>
            <std>0.00549248</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.0</x>
            <y units="&#8491;">2.0</y>
            <z units="&#8491;">2.0</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0067</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of TBC-DEG:TBCC:tubulin complex</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6393::::</details>
    </map>
</emd>