<emd emdb_id="EMD-6218" 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>2014-12-15</deposition>
            <header_release>2014-12-24</header_release>
            <map_release>2015-12-16</map_release>
            <update>2016-02-10</update>
        </key_dates>
        <title>Yeast Rvb1 and Rvb2 proteins oligomerize as a conformationally variable dodecamer with low frequency</title>
        <authors_list>
            <author>Jeganathan A</author>
            <author>Leong A</author>
            <author>Huen J</author>
            <author>Zhao L</author>
            <author>Nano N</author>
            <author>Houry WA</author>
            <author>Ortega J</author>
        </authors_list>
        <keywords>AAA+, Electron microscopy, Pontin, Reptin, Chromatin remodeling</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Jeganathan A</author>
                    <author order="2">Leong V</author>
                    <author order="3">Zhao L</author>
                    <author order="4">Huen J</author>
                    <author order="5">Nano N</author>
                    <author order="6">Houry WA</author>
                    <author order="7">Ortega J</author>
                    <title>Yeast rvb1 and rvb2 proteins oligomerize as a conformationally variable dodecamer with low frequency.</title>
                    <journal>J.MOL.BIOL.</journal>
                    <volume>427</volume>
                    <first_page>1875</first_page>
                    <last_page>1886</last_page>
                    <year>2015</year>
                    <external_references type="PUBMED">25636407</external_references>
                    <external_references type="DOI">doi:10.1016/j.jmb.2015.01.010</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>In vivo assembled Rvb1/Rvb2 complex, CL4</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>In vivo assembled Rvb1/Rvb2 complex, CL4</name>
                <oligomeric_state>6 molecules of Rvb1 and 6 molecules of Rvb2</oligomeric_state>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.6</experimental>
                    <theoretical units="MDa">0.6</theoretical>
                    <method>Size exclusion chromatography</method>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="RuvBL1, Tip49a, Tip48 / Tip49, ECP-54, Pontin, Tih1, p50, Tap54b">Rvb1</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                    <synonym_organism>Yeast</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.0505</experimental>
                    <theoretical units="MDa">0.0505</theoretical>
                </molecular_weight>
                <number_of_copies>6</number_of_copies>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>BL21(DE3) pRIL</recombinant_strain>
                    <recombinant_plasmid>pCOLADuet-1</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">Q03940</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name synonym="RuvBL2, Tip49b, Tip49 / Tip48, ECP-51, Reptin, Tih2, p47, Tap54a">Rvb2</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                    <synonym_organism>Yeast</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.0516</experimental>
                    <theoretical units="MDa">0.0516</theoretical>
                </molecular_weight>
                <number_of_copies>6</number_of_copies>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>BL21(DE3) pRIL</recombinant_strain>
                    <recombinant_plasmid>pCOLADuet-1</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">Q12464</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>7.5</ph>
                        <details>25 mM Tris-HCl, pH 7.5, 80 mM KCl, 10% v/v glycerol, 1 mM DTT</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>2% uranyl acetate</details>
                    </staining>
                    <grid>
                        <details>400 mesh grids with thin carbon support, glow-discharged in air atmosphere</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 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">1</nominal_cs>
                    <nominal_defocus_min units="&#181;m">2.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.0</nominal_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <specimen_holder_model>JEOL</specimen_holder_model>
                    <date>2014-02-01</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>NIKON SUPER COOLSCAN 9000</scanner>
                                <sampling_interval units="&#181;m">12.7</sampling_interval>
                            </digitization_details>
                            <number_real_images>100</number_real_images>
                            <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>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Particles selected with boxer, image classification done using ML3D, and projection matching 3D reconstruction done with Xmipp.</details>
                <ctf_correction>
                    <details>CTFFIND3</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">25.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Xmipp</name>
                        </software>
                    </software_list>
                    <number_images_used>1718</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="6751">
        <file>emd_6218.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>120</col>
            <row>120</row>
            <sec>120</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>120</x>
            <y>120</y>
            <z>120</z>
        </spacing>
        <cell>
            <a units="&#8491;">304.8</a>
            <b units="&#8491;">304.8</b>
            <c units="&#8491;">304.8</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>-0.03619136</minimum>
            <maximum>0.0853504</maximum>
            <average>-0.0005509</average>
            <std>0.00898988</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.54</x>
            <y units="&#8491;">2.54</y>
            <z units="&#8491;">2.54</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.018</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>In vivo assembled yeast Rvb1/Rvb2 complex (dodecamer, CL4)</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6218::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_6218.png</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>