<emd emdb_id="EMD-5915" 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>2014-03-01</deposition>
            <header_release>2014-03-12</header_release>
            <map_release>2014-04-30</map_release>
            <update>2014-05-21</update>
        </key_dates>
        <title>The structure of a complete multidrug efflux pump</title>
        <authors_list>
            <author>Du D</author>
            <author>Wang Z</author>
            <author>James NR</author>
            <author>Voss JE</author>
            <author>Klimont E</author>
            <author>Ohene-Agyei T</author>
            <author>Venter H</author>
            <author>Chiu W</author>
            <author>Luisi BF</author>
        </authors_list>
        <keywords>multidrug efflux pump</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Du D</author>
                    <author order="2">Wang Z</author>
                    <author order="3">James NR</author>
                    <author order="4">Voss JE</author>
                    <author order="5">Klimont E</author>
                    <author order="6">Ohene-Agyei T</author>
                    <author order="7">Venter H</author>
                    <author order="8">Chiu W</author>
                    <author order="9">Luisi BF</author>
                    <title>Structure of the AcrAB-TolC multidrug efflux pump</title>
                    <journal>NATURE</journal>
                    <volume>509</volume>
                    <first_page>512</first_page>
                    <last_page>515</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">24747401</external_references>
                    <external_references type="DOI">doi:10.1038/nature13205</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>AcrB-AcrA-TolC-AcrZ multidrug efflux pump</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>AcrB-AcrA-TolC-AcrZ multidrug efflux pump</name>
                <oligomeric_state>One homotrimer of TolC and one homotrimer of AcrB bound to a homohexamer of AcrA; three AcrZ molecules are bound to the AcrB</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">0.771</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="acridine transport pump">AcrABZ-TolC complex</name>
                <natural_source database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                    <strain>W3110</strain>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.77</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <oligomeric_state>hetero-pentadecamer (15-mer)</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism>Escherichia coli.</recombinant_organism>
                    <recombinant_strain>C43 (DE3)</recombinant_strain>
                    <recombinant_plasmid>pET21a and pRSFDuet-1</recombinant_plasmid>
                </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">2.0</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>50 mM HEPES pH 7.5, 400 mM NaCl, 0.03% DDM</details>
                    </buffer>
                    <grid>
                        <details>200 mesh copper grid with holey carbon film</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>Blot 1 second at force 0</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 3200FSC</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>DARK FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <nominal_defocus_min units="&#181;m">0.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.5</nominal_defocus_max>
                    <nominal_magnification>20000.0</nominal_magnification>
                    <specimen_holder_model>JEOL 3200FSC CRYOHOLDER</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">78</temperature_min>
                        <temperature_max units="K">80</temperature_max>
                        <temperature_average units="K">79</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 100k magnification</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <specialist_optics>
                        <energy_filter>
                            <name>JEOL</name>
                        </energy_filter>
                    </specialist_optics>
                    <date>2013-05-20</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">DIRECT ELECTRON DE-12 (4k x 3k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">6</sampling_interval>
                            </digitization_details>
                            <number_real_images>1281</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">25</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Particle were selected by eman2 e2boxer. Initial model was generated by eman2 base on reference free 2d class averages. Further refinements were done by eman2.07, followed by Relion at the end.</details>
                <ctf_correction>
                    <details>per image</details>
                </ctf_correction>
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">15.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN2, RELION</name>
                        </software>
                    </software_list>
                    <details>Resolution was estimated by gold standard eotest from two independent reconstructions.</details>
                    <number_images_used>7000</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="65537">
        <file>emd_5915.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>256</col>
            <row>256</row>
            <sec>256</sec>
        </dimensions>
        <origin>
            <col>-128</col>
            <row>-128</row>
            <sec>-128</sec>
        </origin>
        <spacing>
            <x>256</x>
            <y>256</y>
            <z>256</z>
        </spacing>
        <cell>
            <a units="&#8491;">632.32</a>
            <b units="&#8491;">632.32</b>
            <c units="&#8491;">632.32</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>-10.050803180000001</minimum>
            <maximum>25.346019739999999</maximum>
            <average>0.0</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.47</x>
            <y units="&#8491;">2.47</y>
            <z units="&#8491;">2.47</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>7.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of complete multidrug efflux pump</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5915::::</details>
    </map>
</emd>