<emd emdb_id="EMD-6642" 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>2016-05-03</deposition>
            <header_release>2016-07-13</header_release>
            <map_release>2017-05-03</map_release>
            <update>2017-05-03</update>
        </key_dates>
        <title>Cryo-EM structure of the WRC-Rac1 complex</title>
        <authors_list>
            <author>Chen B</author>
            <author>Chou H-T</author>
            <author>Xing W</author>
            <author>Henry L</author>
            <author>Walz T</author>
            <author>Rosen MK</author>
        </authors_list>
        <keywords>cryoelectron microscopy, Wave Regulatory Complex, GTPase, actin nucleation</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Chen B</author>
                    <author order="2">Chou H-T</author>
                    <author order="3">Xing W</author>
                    <author order="4">Henry L</author>
                    <author order="5">Walz T</author>
                    <author order="6">Rosen MK</author>
                    <title>Rac1 GTPase Activates the WAVE Regulatory Complex Through Two Distinct Binding Sites</title>
                    <journal>To Be Published</journal>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Complex of WAVE regulatory complex (WRC) and Rac1</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Complex of WAVE regulatory complex (WRC) and Rac1</name>
                <details>The sample was monodisperse.</details>
                <oligomeric_state>One heteropentamer of WRC binds to one Rac1</oligomeric_state>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">0.375</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="WRC">WAVE regulatory complex</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.375</theoretical>
                </molecular_weight>
                <details>WRC is composed of 5 subunits: Sra1, Nap1, WAVE1, Abi2, and HSPC300.</details>
                <number_of_copies>1</number_of_copies>
                <oligomeric_state>heterohexamer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="7108">Spodoptera frugiperda</recombinant_organism>
                    <recombinant_cell>sf9</recombinant_cell>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>Rac1</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                </natural_source>
                <details>Rac1 is fused to C-terminal WAVE1.</details>
                <number_of_copies>1</number_of_copies>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="7108">Spodoptera frugiperda</recombinant_organism>
                    <recombinant_cell>sf9</recombinant_cell>
                </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">0.1</concentration>
                    <buffer>
                        <ph>7.0</ph>
                        <details>10 mM HEPES, 100 mM NaCl, 1 mM MgCl2, 2 mM TCEP</details>
                    </buffer>
                    <grid>
                        <details>glow-discharged Quantifoil holey carbon grids (400 copper mesh, R1.2/1.3)</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">80</chamber_humidity>
                        <chamber_temperature units="K">103</chamber_temperature>
                        <instrument>GATAN CRYOPLUNGE 3</instrument>
                        <method>WRC-Rac1 complex (3.5 microliter at 0.1 mg/ml) was applied to glow-discharged Quantifoil holey carbon grids (400 copper mesh, R1.2/1.3). The grids were blotted for 3 seconds and quick-frozen in liquid ethane using a Gatan CryoPlunge 3.</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI 20</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">1.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.5</nominal_defocus_max>
                    <nominal_magnification>29000.0</nominal_magnification>
                    <calibrated_magnification>40410.0</calibrated_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">88</temperature_average>
                    </temperature>
                    <date>2015-06-16</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">5</sampling_interval>
                            </digitization_details>
                            <number_real_images>2173</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">38.4</average_electron_dose_per_image>
                            <details>There were a total of 2,173 image stacks. For 1,366 stacks, 30 frames were recorded at 200 ms per frame (total exposure time of 6 seconds). For 407 stacks, 34 frames were recorded at 300 ms per frame (total exposure time of 10.2 seconds). For 400 stacks, 51 frames were recorded at 200 ms per frame (total exposure time of 10.2 seconds).</details>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>This holder operates at liquid nitrogen temperature.</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Initial model was low-pass filtered crystal structure of the WRC complex (PDB ID 3P8C). Automatic particle picking, 2D classification, 3D classification, refinement, and subsequent reconstruction were performed using RELION.</details>
                <ctf_correction>
                    <details>whole micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">7.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Relion</name>
                        </software>
                    </software_list>
                    <number_images_used>29784</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="61037">
        <file>emd_6642.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>250</col>
            <row>250</row>
            <sec>250</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>250</x>
            <y>250</y>
            <z>250</z>
        </spacing>
        <cell>
            <a units="&#8491;">310.0</a>
            <b units="&#8491;">310.0</b>
            <c units="&#8491;">310.0</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>-0.03580169</minimum>
            <maximum>0.08824085</maximum>
            <average>0.00030724</average>
            <std>0.00353338</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.24</x>
            <y units="&#8491;">1.24</y>
            <z units="&#8491;">1.24</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0217</level>
                <source>EMDB</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of WRC-Rac1</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6642::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3P8C</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <refinement_space>REAL</refinement_space>
            </modelling>
            <modelling>
                <initial_model>
                    <access_code>3SBD</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>