<emd emdb_id="EMD-6084" 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>2014-09-02</deposition>
            <header_release>2014-10-01</header_release>
            <map_release>2014-10-22</map_release>
            <update>2014-11-19</update>
        </key_dates>
        <title>Anaphase Promoting Complex with bound Ube2S</title>
        <authors_list>
            <author>Brown NG</author>
            <author>Watson ER</author>
            <author>Weissmann F</author>
            <author>Jarvis MA</author>
            <author>Vanderlinden R</author>
            <author>Grace CRR</author>
            <author>Frye JJ</author>
            <author>Qiao R</author>
            <author>Dube P</author>
            <author>Petzold G</author>
            <author>Cho SE</author>
            <author>Alsharif O</author>
            <author>Bao J</author>
            <author>Davidson IF</author>
            <author>Zheng J</author>
            <author>Nourse A</author>
            <author>Kurinov I</author>
            <author>Peters JM</author>
            <author>Stark H</author>
            <author>Schulman BA</author>
        </authors_list>
        <keywords>Anaphase Promoting Complex, APC/C, Ube2s, Ubiquitination</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Brown NG</author>
                    <author order="2">Watson ER</author>
                    <author order="3">Weissmann F</author>
                    <author order="4">Jarvis MA</author>
                    <author order="5">VanderLinden R</author>
                    <author order="6">Grace CR</author>
                    <author order="7">Frye JJ</author>
                    <author order="8">Qiao R</author>
                    <author order="9">Dube P</author>
                    <author order="10">Petzold G</author>
                    <author order="11">Cho SE</author>
                    <author order="12">Alsharif O</author>
                    <author order="13">Bao J</author>
                    <author order="14">Davidson IF</author>
                    <author order="15">Zheng JJ</author>
                    <author order="16">Nourse A</author>
                    <author order="17">Kurinov I</author>
                    <author order="18">Peters JM</author>
                    <author order="19">Stark H</author>
                    <author order="20">Schulman BA</author>
                    <title>Mechanism of Polyubiquitination by Human Anaphase-Promoting Complex: RING Repurposing for Ubiquitin Chain Assembly.</title>
                    <journal>MOLECULAR CELL</journal>
                    <volume>56</volume>
                    <first_page>246</first_page>
                    <last_page>260</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">25306923</external_references>
                    <external_references type="DOI">doi:10.1016/j.molcel.2014.09.009</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Anaphase promoting complex with bound Ube2S</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Anaphase promoting complex with bound Ube2S</name>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">1.5</experimental>
                    <theoretical units="MDa">1.5</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="APC/C">Anaphase Promoting Complex</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">1.5</experimental>
                    <theoretical units="MDa">1.5</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name synonym="Ube2S">Ubiquitin-conjugating enzyme E2 S</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">
                    <buffer>
                        <ph>8.0</ph>
                        <details>20 mM HEPES, pH 8.0, 200 mM NaCl</details>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">95</chamber_humidity>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</microscope>
                    <illumination_mode>SPOT SCAN</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">0</nominal_cs>
                    <nominal_defocus_min units="&#181;m">2.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">5.0</nominal_defocus_max>
                    <calibrated_magnification>74000.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">80</temperature_min>
                    </temperature>
                    <date>2014-03-05</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">FEI FALCON II (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">25</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </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;">23.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>in_house_software, Relion</name>
                        </software>
                    </software_list>
                    <number_images_used>18314</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="3908">
        <file>emd_6084.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>100</col>
            <row>100</row>
            <sec>100</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>100</x>
            <y>100</y>
            <z>100</z>
        </spacing>
        <cell>
            <a units="&#8491;">400.0</a>
            <b units="&#8491;">400.0</b>
            <c units="&#8491;">400.0</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>-32.929710389999997</minimum>
            <maximum>110.288986210000004</maximum>
            <average>1.53413892</average>
            <std>8.48929882</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">4.0</x>
            <y units="&#8491;">4.0</y>
            <z units="&#8491;">4.0</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>29.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>3D reconstruction of the Anaphase Promoting Complex with bound Ube2S - second conformation</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6084::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>1ZDN</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>