<emd emdb_id="EMD-5381" 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>2012-01-08</deposition>
            <header_release>2012-01-11</header_release>
            <map_release>2012-03-14</map_release>
            <update>2014-06-04</update>
        </key_dates>
        <title>Cdc6-induced Conformational Changes in ORC Bound To Origin DNA Revealed by Cryo-Electron Microscopy. This map may be mirrored (based on comparison to EMD-5625).</title>
        <authors_list>
            <author>Sun J</author>
            <author>Kawakami H</author>
            <author>Zech J</author>
            <author>Speck C</author>
            <author>Stillman B</author>
            <author>Li H</author>
        </authors_list>
        <keywords>ORC, Cdc6</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Sun J</author>
                    <author order="2">Kawakami H</author>
                    <author order="3">Zech J</author>
                    <author order="4">Speck C</author>
                    <author order="5">Stillman B</author>
                    <author order="6">Li H</author>
                    <title>Cdc6-induced conformational changes in ORC bound to origin DNA revealed by cryo-electron microscopy.</title>
                    <journal>STRUCTURE</journal>
                    <volume>20</volume>
                    <first_page>534</first_page>
                    <last_page>544</last_page>
                    <year>2012</year>
                    <external_references type="PUBMED">22405012</external_references>
                    <external_references type="DOI">doi:10.1016/j.str.2012.01.011</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Yeast Origin Recognition Complex with dsDNA and Cdc6</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Yeast Origin Recognition Complex with dsDNA and Cdc6</name>
                <details>ORC and Cdc6 are mixed with 66 bp DNA with ARS1 in ATPrS</details>
                <number_unique_components>8</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.5</experimental>
                    <theoretical units="MDa">0.5</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="ORC, Cdc6">Yeast Origin Recognition Complex and Cdc6</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                    <synonym_organism>ORC, Cdc6</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.5</experimental>
                    <theoretical units="MDa">0.5</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="4932">Saccharomyces cerevisiae</recombinant_organism>
                    <recombinant_plasmid>pCITE-2a</recombinant_plasmid>
                </recombinant_expression>
                <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">0.4</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>50 mM HEPES/KOH, pH 7.5, 1 mM EDTA, 1 mM EGTA, 1 mM DTT, 100 mM KGlu</details>
                    </buffer>
                    <grid>
                        <details>300 mesh lacey grid with thin continuous carbon</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">70</chamber_humidity>
                        <instrument>OTHER</instrument>
                        <details>Vitrification instrument: FEI Vitrobot</details>
                        <method>Blot 5 seconds</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 2010F</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</nominal_cs>
                    <nominal_defocus_min units="&#181;m">3.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">8.0</nominal_defocus_max>
                    <nominal_magnification>60000.0</nominal_magnification>
                    <calibrated_magnification>60000.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>NIKON COOLSCAN</scanner>
                                <sampling_interval units="&#181;m">6.35</sampling_interval>
                            </digitization_details>
                            <average_electron_dose_per_image units="e/&#8491;^2">15</average_electron_dose_per_image>
                            <bits_per_pixel>8.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Gatan 626200</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>Each particle set</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">15.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN1.8</name>
                        </software>
                    </software_list>
                    <number_images_used>54000</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="433">
        <file>emd_5381.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>48</col>
            <row>48</row>
            <sec>48</sec>
        </dimensions>
        <origin>
            <col>-24</col>
            <row>-24</row>
            <sec>-24</sec>
        </origin>
        <spacing>
            <x>48</x>
            <y>48</y>
            <z>48</z>
        </spacing>
        <cell>
            <a units="&#8491;">203.04001</a>
            <b units="&#8491;">203.04001</b>
            <c units="&#8491;">203.04001</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>-0.47482175</minimum>
            <maximum>7.11127949</maximum>
            <average>0.21266665</average>
            <std>0.72353882</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">4.23</x>
            <y units="&#8491;">4.23</y>
            <z units="&#8491;">4.23</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>cryoEM structure of Yeast Origin Recognition complex with dsDNA and Cdc6. This map may be mirrored (based on comparison to EMD-5625).</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5381::::</details>
    </map>
</emd>