<emd emdb_id="EMD-5614" 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>2013-03-21</deposition>
            <header_release>2013-04-03</header_release>
            <map_release>2013-05-15</map_release>
            <update>2013-06-05</update>
        </key_dates>
        <title>Yeast 20S proteasome with C-terminal peptide of yeast Rpt4</title>
        <authors_list>
            <author>Li X</author>
            <author>Kim HM</author>
            <author>Cheng Y</author>
        </authors_list>
        <keywords>Yeast 20S proteasome, C-terminal peptide, yeast Rpt4</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Park S</author>
                    <author order="2">Li X</author>
                    <author order="3">Kim HM</author>
                    <author order="4">Singh CR</author>
                    <author order="5">Tian G</author>
                    <author order="6">Hoyt MA</author>
                    <author order="7">Lovell S</author>
                    <author order="8">Battaile KP</author>
                    <author order="9">Zolkiewski M</author>
                    <author order="10">Coffino P</author>
                    <author order="11">Roelofs J</author>
                    <author order="12">Cheng Y</author>
                    <author order="13">Finley D</author>
                    <title>Reconfiguration of the proteasome during chaperone-mediated assembly.</title>
                    <journal>NATURE</journal>
                    <volume>497</volume>
                    <first_page>512</first_page>
                    <last_page>516</last_page>
                    <year>2013</year>
                    <external_references type="PUBMED">23644457</external_references>
                    <external_references type="DOI">doi:10.1038/nature12123</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Yeast 20S proteasome</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Yeast 20S proteasome</name>
                <oligomeric_state>28mer</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.7</experimental>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>20S proteasome</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                    <synonym_organism>Baker's yeast</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.7</experimental>
                </molecular_weight>
                <details>GST tag was added to C-terminus of beta-2 subunit</details>
                <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">
                    <grid>
                        <details>Quantifoil Grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">120</chamber_temperature>
                        <instrument>FEI VITROBOT MARK III</instrument>
                    </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">2.1</nominal_defocus_max>
                    <nominal_magnification>100000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <details>Low-Dose procedure</details>
                    <date>2010-01-01</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">TVIPS TEMCAM-F816 (8k x 8k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">25</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>CT3500</specimen_holder>
                    <tilt_angle_min>0</tilt_angle_min>
                    <tilt_angle_max>0</tilt_angle_max>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>FREALIGN</details>
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">7.8</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>FREALIGN</name>
                        </software>
                    </software_list>
                    <number_images_used>36303</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="31251">
        <file>emd_5614.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>200</col>
            <row>200</row>
            <sec>200</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>200</x>
            <y>200</y>
            <z>200</z>
        </spacing>
        <cell>
            <a units="&#8491;">294.0</a>
            <b units="&#8491;">294.0</b>
            <c units="&#8491;">294.0</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>-1.19386077</minimum>
            <maximum>2.49575472</maximum>
            <average>-0.02869725</average>
            <std>0.17732443</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.47</x>
            <y units="&#8491;">1.47</y>
            <z units="&#8491;">1.47</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.8</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>3D density map of yeast 20S proteasome core particle with GST tag added to the C-terminus of beta-2 subunit in complex with the C-terminal peptide of yeast Rpt4</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5614::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>1RYP</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>