<emd emdb_id="EMD-5606" 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>2013-03-10</deposition>
            <header_release>2013-03-20</header_release>
            <map_release>2013-05-01</map_release>
            <update>2013-06-19</update>
        </key_dates>
        <title>Substrate-specific structural rearrangements of human Dicer</title>
        <authors_list>
            <author>Taylor DW</author>
            <author>Ma E</author>
            <author>Shigematsu H</author>
            <author>Cianfrocco MA</author>
            <author>Noland CL</author>
            <author>Nagayama K</author>
            <author>Nogales E</author>
            <author>Doudna JA</author>
            <author>Wang HW</author>
        </authors_list>
        <keywords>RNA-mediated gene silencing, pre-miRNA processing, RNaseIII</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Taylor DW</author>
                    <author order="2">Ma E</author>
                    <author order="3">Shigematsu H</author>
                    <author order="4">Cianfrocco MA</author>
                    <author order="5">Noland CL</author>
                    <author order="6">Nagayama K</author>
                    <author order="7">Nogales E</author>
                    <author order="8">Doudna JA</author>
                    <author order="9">Wang HW</author>
                    <title>Substrate-specific structural rearrangements of human Dicer.</title>
                    <journal>NAT.STRUCT.MOL.BIOL.</journal>
                    <volume>20</volume>
                    <first_page>662</first_page>
                    <last_page>670</last_page>
                    <year>2013</year>
                    <external_references type="PUBMED">23624860</external_references>
                    <external_references type="DOI">doi:10.1038/nsmb.2564</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Human Dicer-PACT heterodimer in open conformation</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Human Dicer-PACT heterodimer in open conformation</name>
                <oligomeric_state>monomer</oligomeric_state>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">0.260</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="Dicer, Helicase with RNase motif">Endoribonuclease Dicer</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.220</theoretical>
                </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" />
                <sequence>
                    <external_references type="UNIPROTKB">Q9UPY3</external_references>
                    <external_references type="GO">GO:0031054</external_references>
                    <external_references type="INTERPRO">IPR000999</external_references>
                    <external_references type="INTERPRO">IPR003100</external_references>
                    <external_references type="INTERPRO">IPR001650</external_references>
                    <external_references type="INTERPRO">IPR014001</external_references>
                    <external_references type="INTERPRO">IPR014720</external_references>
                    <external_references type="INTERPRO">IPR001159</external_references>
                    <external_references type="INTERPRO">IPR011545</external_references>
                    <external_references type="INTERPRO">IPR005034</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name synonym="PACT">Interferon-inducible double stranded RNA-dependent protein kinase activator A</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.034</theoretical>
                </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" />
                <sequence>
                    <external_references type="UNIPROTKB">O75569</external_references>
                    <external_references type="GO">GO:0003725</external_references>
                    <external_references type="INTERPRO">IPR001159</external_references>
                    <external_references type="INTERPRO">IPR014720</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">
                    <concentration units="mg/mL">0.01</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <details>20 mM HEPES, pH 7.5, 150 mM KCl, 3 mM EDTA, 1 mM DTT, and 2.5% glycerol</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>After adsorption for 1 min, we stained the samples consecutively with three droplets of 2% (w/v) uranyl formate solution, blotted off the residual stain and air-dried the sample in a hood.</details>
                    </staining>
                    <grid>
                        <details>glow-discharged holey carbon grids with a thin layer of carbon over the holes</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 TECNAI 12</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <nominal_cs units="mm">5.2</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.4</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">1.5</nominal_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 100,000 times magnification</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2012-07-10</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GENERIC TVIPS (4k x 4k)</film_or_detector_model>
                            <number_real_images>400</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</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 micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">26.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN2/SPARX, multi-model</name>
                        </software>
                    </software_list>
                    <number_images_used>10000</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="2001">
        <file>emd_5606.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>80</col>
            <row>80</row>
            <sec>80</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>80</x>
            <y>80</y>
            <z>80</z>
        </spacing>
        <cell>
            <a units="&#8491;">348.80002</a>
            <b units="&#8491;">348.80002</b>
            <c units="&#8491;">348.80002</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>-4.73826694</minimum>
            <maximum>19.24861336</maximum>
            <average>0.0</average>
            <std>0.99999905</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">4.36</x>
            <y units="&#8491;">4.36</y>
            <z units="&#8491;">4.36</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>4.83</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Negative stain EM reconstruction of Dicer-PACT in the open conformation</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5606::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_5606.png</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>