<emd emdb_id="EMD-5630" 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>2013-04-05</deposition>
            <header_release>2013-04-17</header_release>
            <map_release>2013-08-14</map_release>
            <update>2014-03-26</update>
        </key_dates>
        <title>Cryo-electron tomography of in situ flagellar motor of Borrelia burgdorferi FlgC mutant</title>
        <authors_list>
            <author>Zhao X</author>
            <author>Zhang K</author>
            <author>Boquoi T</author>
            <author>Hu B</author>
            <author>Motaleb MA</author>
            <author>Miller KA</author>
            <author>James ME</author>
            <author>Charon NW</author>
            <author>Manson MD</author>
            <author>Norris SJ</author>
            <author>Li C</author>
            <author>Liu J</author>
        </authors_list>
        <keywords>Flagellar motor, assembly, Type III secretion, Lyme disease spirochete, molecular machine</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Zhao X</author>
                    <author order="2">Zhang K</author>
                    <author order="3">Boquoi T</author>
                    <author order="4">Hu B</author>
                    <author order="5">Motaleb MA</author>
                    <author order="6">Miller KA</author>
                    <author order="7">James ME</author>
                    <author order="8">Charon NW</author>
                    <author order="9">Manson MD</author>
                    <author order="10">Norris SJ</author>
                    <author order="11">Li C</author>
                    <author order="12">Liu J</author>
                    <title>Cryoelectron tomography reveals the sequential assembly of bacterial flagella in Borrelia burgdorferi.</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <volume>110</volume>
                    <first_page>14390</first_page>
                    <last_page>14395</last_page>
                    <year>2013</year>
                    <external_references type="PUBMED">23940315</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1308306110</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-5627</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-5628</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-5629</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-5631</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-5632</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-5633</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>In situ flagellar motor from B. burgdorferi FlgC mutant cells</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>In situ flagellar motor from B. burgdorferi FlgC mutant cells</name>
                <number_unique_components>20</number_unique_components>
            </sample_supramolecule>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name>flagellar motor</name>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <natural_source database="NCBI">
                    <organism ncbi="139">Borrelia burgdorferi</organism>
                    <strain>B31</strain>
                    <synonym_organism>Lyme disease spirochete</synonym_organism>
                </natural_source>
                <recombinant_expression database="NCBI" />
            </organelle_or_cellular_component_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>subtomogramAveraging</method>
            <aggregation_state>cell</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <details>BSK-II liquid medium supplemented with 6% rabbit serum</details>
                    </buffer>
                    <grid>
                        <details>freshly glow-discharged holey carbon grids</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <method>Bacterial culture was deposited onto freshly glow-discharged, holey carbon grids for 1 min. Grids were blotted with filter paper and then rapidly frozen in liquid ethane, using a homemade gravity-driven plunger apparatus.</method>
                    </vitrification>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_microscopy microscopy_id="1">
                    <microscope>FEI POLARA 300</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <nominal_cs units="mm">2</nominal_cs>
                    <nominal_defocus_min units="&#181;m">6.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">8.0</nominal_defocus_max>
                    <nominal_magnification>31000.0</nominal_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">170</temperature_min>
                    </temperature>
                    <date>2012-05-01</date>
                    <image_recording_list>
                        <image_recording>
                            <number_real_images>21315</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">100</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">-65</min_angle>
                            <max_angle units="deg">65</max_angle>
                        </axis1>
                    </tilt_series>
                </subtomogram_averaging_microscopy>
            </microscopy_list>
            <subtomogram_averaging_processing image_processing_id="1">
                <details>The subvolumes of the flagellar motors were extracted computationally from the tomograms and were further aligned in 3D.</details>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">38.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>IMOD, Raptor, Protomo</name>
                        </software>
                    </software_list>
                    <number_subtomograms_used>999</number_subtomograms_used>
                </final_reconstruction>
                <final_three_d_classification>
                    <number_classes>4</number_classes>
                </final_three_d_classification>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="65537">
        <file>emd_5630.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>-7</col>
            <row>-7</row>
            <sec>-7</sec>
        </origin>
        <spacing>
            <x>256</x>
            <y>256</y>
            <z>256</z>
        </spacing>
        <cell>
            <a units="&#8491;">1459.2</a>
            <b units="&#8491;">1459.2</b>
            <c units="&#8491;">1459.2</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>-16.016363139999999</minimum>
            <maximum>14.98473072</maximum>
            <average>0.0</average>
            <std>0.99999994</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">5.7</x>
            <y units="&#8491;">5.7</y>
            <z units="&#8491;">5.7</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.5</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Flagellar motor of a FlgC mutant in B. burdorferi</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5630::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_5630.png</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>