<emd emdb_id="EMD-5901" 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>2014-02-12</deposition>
            <header_release>2014-03-05</header_release>
            <map_release>2014-04-09</map_release>
            <update>2016-02-17</update>
        </key_dates>
        <title>3D Reconstruction of Membrane Protein Complex ExbB4-ExbD2</title>
        <authors_list>
            <author>Sverzhinsky A</author>
            <author>Fabre L</author>
            <author>Cottreau AL</author>
            <author>Biot-Pelletier DMP</author>
            <author>Khalil S</author>
            <author>Bostina M</author>
            <author>Rouiller I</author>
            <author>Coulton JW</author>
        </authors_list>
        <keywords>Membrane protein complex, coordinated rearrangement, flexible domain</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Sverzhinsky A</author>
                    <author order="2">Fabre L</author>
                    <author order="3">Cottreau AL</author>
                    <author order="4">Biot-Pelletier DMP</author>
                    <author order="5">Khalil S</author>
                    <author order="6">Bostina M</author>
                    <author order="7">Rouiller I</author>
                    <author order="8">Coulton JW</author>
                    <title>Coordinated Rearrangements between Cytoplasmic and Periplasmic Domains of the Membrane Protein Complex ExbB-ExbD of Escherichia coli</title>
                    <journal>STRUCTURE</journal>
                    <volume>22</volume>
                    <first_page>791</first_page>
                    <last_page>797</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">24657092</external_references>
                    <external_references type="DOI">doi:10.1016/j.str.2014.02.010</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-5902</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-5903</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Membrane protein complex ExbB4-ExbD2 from Escherichia coli</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Membrane protein complex ExbB4-ExbD2 from Escherichia coli</name>
                <oligomeric_state>Four ExbB in complex with two ExbD</oligomeric_state>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">0.139</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="ExbB">Biopolymer Transport Protein ExbB</name>
                <natural_source database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                    <strain>K-12</strain>
                    <cellular_location>Cytoplasmic Membrane</cellular_location>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.026</theoretical>
                </molecular_weight>
                <number_of_copies>4</number_of_copies>
                <oligomeric_state>Tetramer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>M15</recombinant_strain>
                    <recombinant_plasmid>pQE60</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">P0ABU7</external_references>
                    <external_references type="GO">GO:0016021</external_references>
                    <external_references type="INTERPRO">IPR014164</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name synonym="ExbD">Biopolymer Transport Protein ExbD</name>
                <natural_source database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                    <strain>K-12</strain>
                    <cellular_location>Cytoplasmic Membrane</cellular_location>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.017</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>M15</recombinant_strain>
                    <recombinant_plasmid>pQE60</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">P0ABV2</external_references>
                    <external_references type="GO">GO:0016021</external_references>
                    <external_references type="INTERPRO">IPR014170</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">0.02</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>25 mM Tris-HCl, 150 mM NaCl, 0.01% DDM</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>Grids with adsorbed protein were stained with 1.5% uranyl formate for 1 minute.</details>
                    </staining>
                    <grid>
                        <details>400 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 F20</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">2.0</nominal_cs>
                    <nominal_defocus_min units="&#181;m">1.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.5</nominal_defocus_max>
                    <nominal_magnification>67000.0</nominal_magnification>
                    <calibrated_magnification>67147.0</calibrated_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 50,000x magnification</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2013-03-27</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Room temperature</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Manual particle picking from random conical tilt pairs, 3D classification, projection matching angular refinement</details>
                <ctf_correction>
                    <details>Each Micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">21.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Xmipp, EMAN2, SPARX</name>
                        </software>
                    </software_list>
                    <number_images_used>7322</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="8193">
        <file>emd_5901.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>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>128</x>
            <y>128</y>
            <z>128</z>
        </spacing>
        <cell>
            <a units="&#8491;">281.6</a>
            <b units="&#8491;">281.6</b>
            <c units="&#8491;">281.6</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>-0.09642076</minimum>
            <maximum>0.10619523</maximum>
            <average>-0.00112127</average>
            <std>0.01226369</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.2</x>
            <y units="&#8491;">2.2</y>
            <z units="&#8491;">2.2</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.029</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>ExbB4-ExbD2 complex with ExbD periplasmic domains unobservable</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5901::::</details>
    </map>
</emd>