<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-5978" version="3.0.1.9">
    <admin>
        <status_history_list>
            <status status_id="1">
                <code>REL</code>
            </status>
        </status_history_list>
        <current_status>
            <code>OBS</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2014-05-29</deposition>
            <header_release>2014-07-30</header_release>
            <map_release>2015-06-10</map_release>
            <obsolete>2015-06-10</obsolete>
            <update>2015-06-10</update>
        </key_dates>
        <title>3DEM structure of Rrp5</title>
        <authors_list>
            <author>Khoshnevis S</author>
            <author>Askenasy I</author>
            <author>Johnson MC</author>
            <author>Young-Erdos CL</author>
            <author>Karbstein K</author>
            <author>Stroupe ME</author>
        </authors_list>
        <keywords>Rrp5, RNA binding protein, ribosome assembly factor, 40S ribosome, 60S ribosome, Rok1, DEAD-box protein</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Khoshnevis S</author>
                    <author order="2">Askenasy I</author>
                    <author order="3">Johnson MC</author>
                    <author order="4">Young-Erdos CL</author>
                    <author order="5">Karbstein K</author>
                    <author order="6">Stroupe ME</author>
                    <title>ATP Hydrolysis by the DEAD-box protein Rok1 Releases the Assembly Factor Rrp5 from pre-40S Ribosomes.</title>
                    <journal>To Be Published</journal>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-5979</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-5980</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Saccharomyces cerevisiae Rrp5 bound to H45-3ITS1 RNA</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Saccharomyces cerevisiae Rrp5 bound to H45-3ITS1 RNA</name>
                <details>At a 5 sigma contour, the mass is about 0.25 MDa, which corresponds to about 0.2 MDa from Rrp5 and 0.05 MDa from RNA.</details>
                <oligomeric_state>1</oligomeric_state>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">0.35</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="Rrp5, U3 small nucleolar RNA-associated protein RRP5">Ribosomal RNA Processing 5</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                    <strain>By 4741</strain>
                    <synonym_organism>Yeast</synonym_organism>
                    <cellular_location>nucleolus</cellular_location>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.35</experimental>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <oligomeric_state>monomer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>Rosetta2 (DE3)</recombinant_strain>
                    <recombinant_plasmid>pGEX-6-P3</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">Q05022</external_references>
                    <external_references type="GO">GO:0006396</external_references>
                    <external_references type="GO">GO:0003723</external_references>
                    <external_references type="GO">GO:0005515</external_references>
                    <external_references type="GO">GO:0005622</external_references>
                    <external_references type="INTERPRO">IPR012340</external_references>
                    <external_references type="INTERPRO">IPR003029</external_references>
                    <external_references type="INTERPRO">IPR011990</external_references>
                    <external_references type="INTERPRO">IPR003107</external_references>
                </sequence>
            </protein_or_peptide>
            <rna macromolecule_id="2">
                <name synonym="H45-3ITS1 RNA">pre-rRNA</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                    <strain>By 4741</strain>
                    <synonym_organism>yeast</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.12</theoretical>
                </molecular_weight>
                <details>in vitro transcribed</details>
                <classification>OTHER</classification>
                <structure>SINGLE STRANDED</structure>
                <synthetic_flag>false</synthetic_flag>
            </rna>
        </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>6.7</ph>
                        <details>300 mM NaCl, 10 mM MgCl2, 30 mM MES</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>uranyl formate on floated continuous carbon</details>
                    </staining>
                    <grid>
                        <details>400 mesh copper grid, glow-discharged in Gatan Solarus apparatus</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>FEI TITAN KRIOS</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <nominal_defocus_min units="µm">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">3.0</nominal_defocus_max>
                    <nominal_magnification>59000.0</nominal_magnification>
                    <calibrated_magnification>65555.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <date>2013-03-23</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <number_real_images>1200</number_real_images>
                            <average_electron_dose_per_image units="e/Å^2">20</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Particles were initially manually picked to determine de novo class averages and then automatically picked. Initial model was determined with random conical tilt.</details>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">30.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN</name>
                        </software>
                    </software_list>
                    <details>Final maps were calculated from two averaged datasets.</details>
                    <number_images_used>8500</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>50</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="8193">
        <file>emd_5978.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>-23</col>
            <row>-23</row>
            <sec>-23</sec>
        </origin>
        <spacing>
            <x>128</x>
            <y>128</y>
            <z>128</z>
        </spacing>
        <cell>
            <a units="Å">345.6</a>
            <b units="Å">345.6</b>
            <c units="Å">345.6</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>-6.87094307</minimum>
            <maximum>18.12568092</maximum>
            <average>0.0</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">2.7</x>
            <y units="Å">2.7</y>
            <z units="Å">2.7</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>5.81</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of Rrp5:RNA</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5978::::</details>
    </map>
</emd>
