<emd emdb_id="EMD-5525" 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>2012-11-02</deposition>
            <header_release>2012-11-21</header_release>
            <map_release>2012-11-21</map_release>
            <update>2014-05-14</update>
        </key_dates>
        <title>Electron cryo-microscopy of ABC BmrA in 12-fold symmetry rings</title>
        <authors_list>
            <author>Fribourg PF</author>
            <author>Chami M</author>
            <author>Sorzano CO</author>
            <author>Gubellini F</author>
            <author>Marabini R</author>
            <author>Marco S</author>
            <author>Jault JM</author>
            <author>Levy D</author>
        </authors_list>
        <keywords>ABC transporter, exporter, bmra, yvcc, transmembrane protein, reconstitution into lipids, membrane protein</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Fribourg PF</author>
                    <author order="2">Chami M</author>
                    <author order="3">Sorzano CO</author>
                    <author order="4">Gubellini F</author>
                    <author order="5">Marabini R</author>
                    <author order="6">Marco S</author>
                    <author order="7">Jault JM</author>
                    <author order="8">Levy D</author>
                    <title>3D Cryo-Electron Reconstruction of BmrA, a Bacterial Multidrug ABC Transporter in an Inward-Facing Conformation and in a Lipidic Environment.</title>
                    <journal>J.MOL.BIOL.</journal>
                    <volume>426</volume>
                    <first_page>2059</first_page>
                    <last_page>2069</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">24630999</external_references>
                    <external_references type="DOI">doi:10.1016/j.jmb.2014.03.002</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <auxiliary_link_list>
            <auxiliary_link>
                <link>http://umr168.curie.fr/en/research-groups/structural-analysis-membrane-proteins-and-biomimetic-systems-electron-microscopy/str</link>
            </auxiliary_link>
        </auxiliary_link_list>
    </crossreferences>
    <sample>
        <name>BmrA reconstituted at high density into lipid bilayer.</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>BmrA reconstituted at high density into lipid bilayer.</name>
                <oligomeric_state>24 Homodimers of BmrA inserted into lipid bilayer</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">3.12</experimental>
                    <theoretical units="MDa">3.12</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="YvcC">BmrA</name>
                <natural_source database="NCBI">
                    <organism ncbi="1423">Bacillus subtilis</organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">3.12</experimental>
                    <theoretical units="MDa">3.12</theoretical>
                </molecular_weight>
                <details>24 homodimers of inserted into lipid bilayer</details>
                <number_of_copies>24</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_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>7.8</ph>
                        <details>50mM HEPES, 100mM NaCl</details>
                    </buffer>
                    <grid>
                        <details>Ted Pella inc. holey formvar grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <details>specimen linked to a Ni++-NTA-DOGS/DOPC lipid monolayer</details>
                        <method>Blot for 3 seconds before plunging.</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI/PHILIPS CM200FEG</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">2.26</nominal_cs>
                    <nominal_defocus_min units="&#181;m">2.6</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">5.0</nominal_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <calibrated_magnification>50000.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <date>2003-01-01</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>NIKON COOLSCAN</scanner>
                            </digitization_details>
                            <number_real_images>102</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">15</average_electron_dose_per_image>
                            <bits_per_pixel>8.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Xmipp CL2D classification and Projection matching refinement with Invert Fourier 3D reconstruction</details>
                <ctf_correction>
                    <details>Micrograph based</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">23.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>Xmipp</name>
                        </software>
                    </software_list>
                    <number_images_used>1188</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="31251">
        <file>emd_5525.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>200</col>
            <row>200</row>
            <sec>200</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>200</x>
            <y>200</y>
            <z>200</z>
        </spacing>
        <cell>
            <a units="&#8491;">500.0</a>
            <b units="&#8491;">500.0</b>
            <c units="&#8491;">500.0</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>-0.03243274</minimum>
            <maximum>0.06041811</maximum>
            <average>0.00049039</average>
            <std>0.01073864</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.50</x>
            <y units="&#8491;">2.50</y>
            <z units="&#8491;">2.50</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.029</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of BmrA in a lipidic environment. Reconstruction is D12 symmetrized. 24 homodimers of BmrA are inserted into a lipid bilayer.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5525::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3G61</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <details>Protocol: Rigid body</details>
                <target_criteria>Cross correlation factor</target_criteria>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
        <figure_list>
            <figure>
                <file>emd_5525.tif</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>