<emd emdb_id="EMD-6231" 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>2015-01-04</deposition>
            <header_release>2015-01-14</header_release>
            <map_release>2015-01-14</map_release>
            <update>2016-02-10</update>
        </key_dates>
        <title>The export receptor Crm1 forms a dimer to promote nuclear export of HIV RNA</title>
        <authors_list>
            <author>Booth DS</author>
            <author>Cheng Y</author>
            <author>Frankel AD</author>
        </authors_list>
        <keywords>RNA Nuclear Export, HIV-host interactions, Human Crm1, Human Ran, HIV-1 Rev, HIV-1 Rev Response Element</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Booth DS</author>
                    <author order="2">Cheng Y</author>
                    <author order="3">Frankel AD</author>
                    <title>The export receptor Crm1 forms a dimer to promote nuclear export of HIV RNA.</title>
                    <journal>eLife</journal>
                    <volume>3</volume>
                    <first_page>e04121</first_page>
                    <last_page>e04121</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">25486595</external_references>
                    <external_references type="DOI">doi:10.7554/eLife.04121</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>A dimer of human Crm1/RanGTP bound to the HIV Rev-RRE complex</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>A dimer of human Crm1/RanGTP bound to the HIV Rev-RRE complex</name>
                <oligomeric_state>Crm1/RanGTP dimer, HIV-1 Rev homohexamer, HIV-1 RRE monomer</oligomeric_state>
                <number_unique_components>4</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.462</experimental>
                    <theoretical units="MDa">0.457</theoretical>
                    <method>Multi-angle laser light scattering</method>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="Xpo1">Crm1</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                    <organelle>Nucleus, cytoplasm</organelle>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.125</experimental>
                    <theoretical units="MDa">0.124</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <oligomeric_state>Dimer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>BL21(DE3)</recombinant_strain>
                    <recombinant_plasmid>pET19b</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">O14980</external_references>
                    <external_references type="GO">GO:0005487</external_references>
                    <external_references type="GO">GO:0016032</external_references>
                    <external_references type="GO">GO:0019058</external_references>
                    <external_references type="GO">GO:0008536</external_references>
                    <external_references type="INTERPRO">IPR016024</external_references>
                    <external_references type="INTERPRO">IPR011989</external_references>
                    <external_references type="INTERPRO">IPR001494</external_references>
                    <external_references type="INTERPRO">IPR013598</external_references>
                    <external_references type="INTERPRO">IPR014877</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>Ran</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                    <organelle>Nucleus, cytoplasm</organelle>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.026</experimental>
                    <theoretical units="MDa">0.025</theoretical>
                </molecular_weight>
                <details>Mutation of Gln69Leu with guanosine tri-phosphate bound.</details>
                <number_of_copies>2</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>BL21(DE3)</recombinant_strain>
                    <recombinant_plasmid>pET19b</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">P62826</external_references>
                    <external_references type="GO">GO:0005525</external_references>
                    <external_references type="GO">GO:0005487</external_references>
                    <external_references type="GO">GO:0016032</external_references>
                    <external_references type="GO">GO:0019058</external_references>
                    <external_references type="INTERPRO">IPR027417</external_references>
                    <external_references type="INTERPRO">IPR002041</external_references>
                    <external_references type="INTERPRO">IPR005225</external_references>
                    <external_references type="INTERPRO">IPR001806</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name>Rev</name>
                <natural_source database="NCBI">
                    <organism ncbi="11676">Human immunodeficiency virus 1</organism>
                    <strain>HXB3</strain>
                    <synonym_organism>HIV-1</synonym_organism>
                    <organelle>Nucleus, cytoplasm of host human cells</organelle>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.013</theoretical>
                </molecular_weight>
                <number_of_copies>6</number_of_copies>
                <oligomeric_state>Hexamer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>BL21(DE3)</recombinant_strain>
                    <recombinant_plasmid>pHGB1</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">P04618</external_references>
                    <external_references type="GO">GO:0016032</external_references>
                    <external_references type="GO">GO:0019058</external_references>
                    <external_references type="GO">GO:0051028</external_references>
                    <external_references type="GO">GO:0003723</external_references>
                    <external_references type="GO">GO:0042025</external_references>
                    <external_references type="GO">GO:0030430</external_references>
                    <external_references type="GO">GO:0005515</external_references>
                    <external_references type="INTERPRO">IPR000625</external_references>
                </sequence>
            </protein_or_peptide>
            <rna macromolecule_id="4">
                <name synonym="RRE">Rev Response Element</name>
                <natural_source database="NCBI">
                    <organism ncbi="11676">Human immunodeficiency virus 1</organism>
                    <strain>SF-2</strain>
                    <synonym_organism>HIV-1</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.080</theoretical>
                </molecular_weight>
                <details>245-nucleotide portion of the 351-nucleotide Rev Response Element from the HIV-1 genome</details>
                <sequence>
                    <string>GGGCUAGUAGGAGCUAUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGUGUCAUUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAACAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAGGGAUCAACAGCUCCUAGGGG</string>
                </sequence>
                <classification>OTHER</classification>
                <structure>SINGLE STRANDED</structure>
                <synthetic_flag>true</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">
                    <concentration units="mg/mL">0.1</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <details>50 mM HEPES-KOH, 50 mM potassium chloride, 2 mM magnesium acetate, 2 mM 2-mercaptoethanol, 2% v/v glycerol</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>0.75% w/v uranyl formate</details>
                    </staining>
                    <grid>
                        <details>200 mesh copper grid with thin carbon support, glow discharged</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">2</nominal_cs>
                    <nominal_defocus_min units="&#181;m">1.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">6.0</nominal_defocus_max>
                    <nominal_magnification>52000.0</nominal_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <alignment_procedure>
                        <legacy>
                            <electron_beam_tilt_params>0</electron_beam_tilt_params>
                        </legacy>
                    </alignment_procedure>
                    <date>2012-12-05</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>44</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">40</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <tilt_angle_min>0</tilt_angle_min>
                    <tilt_angle_max>60</tilt_angle_max>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Random conical tilt reconstructions were generated from samples tilted to 60 degrees using angular parameters from class averages of untilted particles. The structure was further refined by projection matching using both tilted and untilted particles.</details>
                <ctf_correction>
                    <details>Each particle</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>FREALIGN, Spider</name>
                        </software>
                    </software_list>
                    <number_images_used>845</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>5</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="2001">
        <file>emd_6231.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>-40</col>
            <row>-40</row>
            <sec>-40</sec>
        </origin>
        <spacing>
            <x>80</x>
            <y>80</y>
            <z>80</z>
        </spacing>
        <cell>
            <a units="&#8491;">323.2</a>
            <b units="&#8491;">323.2</b>
            <c units="&#8491;">323.2</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>-0.20516232</minimum>
            <maximum>1.0428586</maximum>
            <average>-0.0182145</average>
            <std>0.09284244</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">4.04</x>
            <y units="&#8491;">4.04</y>
            <z units="&#8491;">4.04</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.31</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Random conical tilt reconstruction from negative-stain electron micrographs of a human Crm1/RanGTP dimer bound to the HIV-1 Rev-RRE complex.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6231::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3GB8</access_code>
                    <chain>
                        <chain_id>A</chain_id>
                    </chain>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <details>A human Crm1 dimer was extracted from the unit cell of the crystal structure.</details>
                <target_criteria>Correlation</target_criteria>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>